The IDF should consider this: If Iran has developed a nuclear device, they probably haven’t sufficiently weaponized it yet to fit onto one of their Scud-based missiles. Such a prototype nuclear bomb is simply too large this early in the development process to fit into a 880mm missile. Thus the perfect way to deliver such an oversized bomb is with a ship.
Not only that, but who is to say that the Iranians don’t have one or more weapons smuggled out of the Soviet Union as it was collapsing...
Just because their own home-grown nuke-building efforts are still at a relatively primitive stage does not mean that they haven’t acquired more advanced technology and/or materials from other sources.
My guess, though, is that this is more likely to be a conventional arms (and troops) supply mission to Syria and onward to Hezbollah. If they were to ship such material via conventional freighters, the materials would be subject to interception and confiscation. If, however, they ship them via Iranian warships they may believe that the materials are immune from seizure.
They may also attempt a bit of grandstanding, such as a breach of the blockade of Gaza, or other types of direct confrontations with Israeli naval forces.