If those submarines ever have to fire their (nuclear warhead) missiles that would mean there is no Israel to go back to. It would mean Israel was attacked with WMDs, and even if they got back to Israel they may not have the opportunity to re-load. It is a true 'Samson' operation - you do the deed and then the rest is up to God. There might be no going back. Kind of similar to Russian Cold War naval strategy - like the Kirov class battle-cruisers that had over 300 air-defense missiles and 10 anti-sub launchers that were simply for the purpose of ensuring it survived long enough to launch its 20 Granit missiles at a US carrier. Once they fired those missiles their job was done ...after all, there would be no naval base to return to since it would have long been destroyed by the US. The survival rates for surface combatants - both US (especially Carriers) and Soviet (everything) - was less than a day following the outbreak of a real Cold War conflagration. Weapons very quickly became single use, and thus first use only tactical weapons. Don't use them quick enough following the outbreak of strategic war, and your tactical weapons (e.g. Kirovs, carriers, even submarines since all sorts of nuclear depth charges would be sent via ASW rocket launchers to anything that seemed more than a shoal of fish) become useless quite quickly.
I think the day (may it never happen) that Israel decides to use their nuclear cruise missiles from their submarines will be the day those submarines will never need to go home again. A true Samson effort. A nuclear Iran attacking Israel with just 5 missiles, each targeting a major population center, wouldn't destroy Israel ...but it would never again be the Israel we know or love. Quite different from a nuclear Iran attacking, say, a US or a Russia or a China. Those same 5 nuclear weapons would absolutely ruin the economy of the US/Russia/China, but it would be quite different for Israel. 5 attacks, one in Jerusalem, the next in Tel-Aviv, the third in Haifa, fourth in Rishon Lezion, and the last in Ashdod would be a death blow. The response from Israel to the aggressor would be gehenna on earth, however Israel at that point would be like the Biblical Samson ...killing all of the enemy, but all the same dead.