Syria has direct access to the Mediterranean Sea and is a neighbouring country of Israel and Lebanon, and thus very attractive to any country wanting to enjoy both political and military influence in this region. One of these countries is, to no one's surprise, Iran.
Iran's involvement in financing and arming Hamas and Hizbullah is substantial, and often greatly underestimated. For example, the military wing of Hamas (the Izz ad-Din al-Qassam Brigades) frequently receives Iranian-made weaponry or weaponry acquired by Iran. These shipments usually include various sorts of lighter weaponry that is generally more suitable for Gaza's urban environment. It was also supposed to acquire C-704 anti-ship missiles, which were confiscated by the Israeli Navy onboard the freighter Victoria, and Syrian made 302mm Khaibar-1 'M-302' rockets, which were also intercepted by the Israeli Navy near Sudan's Red Sea coast. Members of Iran's Revolutionary Guard present in Sudan take care of the weapon shipments as they travel from Sudan to Gaza via Egypt. Sudan functions as a middle man here, as they allow the shipments to arrive and agree to see them transported over Sudan's soil. A number of past Israeli raids on such convoys and storage depots inside Sudan thus comes as no surprise.
The reason why a part of the weaponry is held back has to do with the inability to safely store and defend larger weapons systems in Lebanon. Buildings containing such weaponry can only be defended by an integrated network of surface-to-air missile systems (SAMs), something which Hizbullah lacks. Syria on the other hand had one of the most dense air-defence networks in the Middle East before the start of the Civil War. While Syria's SAM network has never managed to shoot down any of the Israeli aircraft striking locations in Syria, it does prove more of a deterrence than having no SAMs to defend your weapons systems at all.
Syria's most modern SAM units, some of which strategically positioned around such storage sites, all remain active. Most of these systems were ordered and received in the past couple of years. Should the SAM network have been completed, these storage sites would have been defended by S-300PMU-2s, Buk-M2s, Pechora-2Ms and Pantsir-S1s. It is unknown if Iran provided funding to allow Syria to buy so much high-grade equipment from Russia, but it at least seems likely.
The first time the Syrian method of smuggling armament was put to test was in 2006. Yet Syria's role in this war went further than just supplying some of the weaponry to Hizbullah; it also actively participated in firing rockets at Israel and might even be responsible for the attack on the INS Hanit, an Israeli Sa'ar 5 class corvette.
The most famous documented usage of Syrian weaponry by Hizbullah was the use of 9M133 Kornet ATGMs to destroy at least five Merkava tanks during the 2006 war. 9M133 missile containers captured by the IDF revealed the true origin of the shipment: Syria.
Direct involvement of Syria in the 2006 conflict came through the use of 302mm Khaibar-1 multiple rocket launchers (MRLs), an indigenous product of Syria. These MRLs, operating from within Lebanon, were responsible for much of the damage done on Israel's infrastructure. While it was initially thought these launchers were only provided by Syria to Hizbullah, all the Khaibar-1s were actually operated by Syria's 158th Missile Regiment in close cooperation with Hizbullah. At least one Khaibar-1 was destroyed by the Israeli Air Force.
Syrian-produced 220mm MRLs also saw use in Lebanon, where they were used by Hizbullah. Most of the launch platforms used for the 220mm and 302mm Khaibar-1 rockets are based on brightly coloured civilian trucks, which can be quickly reconfigured to a more civilian look shortly after launch.
The usage of such trucks is perfect for Hizbullah, as they're very mobile and its deadly weaponry is easy to hide. For example, this Falaq-2 used by Syrian troops in the Syrian Civil War was reconfigured to resemble a civilian truck within minutes after launching its rocket.
The relative ease of driving these trucks around in Lebanon is what caused another major incident: The assault on the INS Hanit by a C-802 (or the Iranian-produced copy by the name of Noor) anti-ship missile fired by Hizbullah, likely aided by members of the Revolutionary Guard. In order to fire a C-802, you need a launch platform, which is either a ship, a plane or a truck. The first two possibilities can be eliminated immediately as Hizbullah doesn't operate any fighter jets or missile boats. This leaves a truck-based launcher as the only remaining option.
Syria is known to have acquired a truck-based C-802 coastal defence system, which was shown in a live firing exercise by the Syrian Navy in 2012. This raises the question if Syria might have been involved in the assault on the C-802 at the INS Hanit.
While Syria was already in the possession of a C-802 based launcher, Hizbullah was not yet familiar with such a system, and would have had trouble storing it within Lebanon. Much more likely is that it was actually Syria who transported one of its C-802 launch platforms (as seen with the 220mm and 302mm rockets) to Lebanon disguised as a civilian truck, and subsequently used it to strike the INS Hanit in cooperation with Hizbullah and the Revolutionary Guard, after which the launch platform safely returned to Syria.
To ease the flow of such sophisticated weaponry, Iran established a production line for Zelzal-2 artillery rockets and Fateh 110 ballistic missiles inside Syria. These production lines are likely based in the undergound facilities of the Al Safir and Hama missile facility sites. In Syria, the Zelzal-2 is known as the 'Maysalun', referring to the Battle of Maysalun which was won by the French. The Fateh 110 is known as the 'Tishreen', which in turn refers to the October War. Syrian artillery rockets and missiles are seen as weapons of revenge and thus always purposely named after military defeats. The Maysalun and the Tishreen can be seen in the images below.
As weapons such as the Zelzal-2, Fateh 110 and C-802 would require a whole new Israeli strategy to cope with such threats, taking out some of the advanced weaponry destined for use with or alongside Hizbullah seems exactly what Israel is doing. By taking out advanced equipment before it even reaches its destination, Hizbullah is derived of offensive capabilities that could otherwise inflict serious damage on the Israeli military, yet while running a low risk of actually provoking a war or suffering losses itself.
If Syria would retaliate by firing ballistic missiles on Israel, it would undoubtedly result in a direct war, which the already battered Syrian military simply isn't capable of waging at this point. Such a war would see the whole Syrian Arab Air Force (SyAAF) destroyed by Israel, leaving a gap easily exploited by groups such as the Free Syrian Army and the Islamic State. This imbalance in military capabilities essentially means has Israel can roam free through Syrian airspace without having to fear serious retaliations.
Syria's inability to protect these shipments against Israeli attacks is the only hitch in the method of covertly providing arms to Hizbullah. As the Israeli Air Force makes heavy use of electronic countermeasures and deploys weapon systems outside the range of Syrian SAM systems, Israel can freely continue to roam over the Syrian skies, at least until Syria receives its first S-300PMU-2.
Buk-M2 SAM systems and Bastion-P coastal defence systems were reported to have been struck out of fear of these weapons falling in the hands of Hizbullah. This has much to do with Israel's fear of a repetition of the INS Hanit scenario.Yet it remains unlikely Syria would use its most advanced Russian SAM systems and coastal defence systems in Lebanon in the foreseeable future. In turn, transferring such large weapon systems to Hizbullah would likely meet fierce resistance from Russia, and thus seems unlikely.
In case of a future war with Israel, we might see an increasing amount of Iranian and Syrian weaponry being used by Hizbullah and by Syria itself within Lebanon. Advanced weaponry such as the Igla-S and Fateh 110 missiles will surely change the way any future war in the region will be fought.
Essentially, both parties are waging a covert war spanning a large period of time. Syria (as well as Iran for that matter) use Hizbullah and other anti-Israel groups in the Middle East as a proxy to fight the war on their own terms, whereas Israel manages to strike at its enemies without any retaliation.