In which case one idea for that would be not overflow, but have one of the ships selected to be 'secondary' and the storage could also exist but not be able add more to it.
Alright, so... if that storage is given a high capacity like Material Storage and everything from the consumed ship gets chucked into that including unsold Personal Shop goods and deployed furnishings and consumed music discs that both get converted back to item form... you'll end up with a huge full secondary storage.
Now, what happens when you need to take things out of that storage? What if the consumed ship was your primary one and has all your room goods so you need to retrieve them to recreate your room? Or your time-limited non-stacking Bonus Keys? Outfits or outerwear you regularly switch between?
This kind of storage definitely alleviates the issue of suddenly giving players 600+ more items than they have space for and locking them out of picking anything up, and I'm glad you thought of it. But it still isn't perfect and it still does nothing about destroyed alliances, ship currencies like CC or other ship-based unlocks that would still be lost. And if that storage has a time limit before they take it away it's just kicking the can down the road.
And to be honest I really do not have faith they'd remember to account for players' registered music discs on the consumed ship. And if not, those of us who spent 3200 SG on music discs in particular would be seriously affected! They can't even revive AC scratches or Mission Pass seasons properly even after knowingly blocking players from several of them, so this sounds like it's expecting way too much of an exercise they'd want to be done with quickly.
Which is the point really. Problematic destructive merges that may need to be repeated in the future don't ultimately solve anything, they just cause grief to perpetuate an outdated server architecture. If they want to properly deal with it, may as well migrate to a modern structure, eliminate sharding in the first place, and use that as a chance to properly work out how to either preserve everything or at the very least affect everyone equally so it's not just players from one ship that get screwed over by what'd effectively be a forced transfer.