Starting naked is one of those ideas that as people say "sounds really good on paper" ...
But once you try to implement them, they become pure obstacle and anoyance. :-/
Even if you put aside main difference ... that some classes, like Barbarian, dont really need to wear any armor to be effectively protected ... while other classes, like Paladin, become squishy like a sponge, without their armor ...
You mentioned storytelling.
So take it from that perspective ...
Where would we take our armors and weapons?
There was some suggestions in the past:
- From corpses of minions (as you said aswell) ... ok, but where they took them? I mean, we are on Nautiloid ship ... there is little to zero (at least known to us at this point) reason for them to be armed, they are not there to form an invading force, they are basicaly just packed food for their Mind Flayer masters.

- From a box where they store it ... ok, but why would they store it in the first place? I mean, again we are on Nautiloid ship and we just got our own tadpole ... that means that we are either becoming Mind Flayer, wich dont use weapons ... or we are becoming thrall, respectively food some time later, wich dont need to be armed as we stated abowe ... or we are becoming a True Soul, wich are meaned to infiltrate important positions and work from there ... ok, this last option could use a weapon, but is it really safe to keep it close before we are brainwashed? Nope its not. :-/
- Just laying on the ground around our pod ... ok, but same problem as with the box, what reason in hell would anyone have to after wasting time with disarming us, just to keep the weapon laying around anywhere?
- From infernals that board the ship ... this is a good one, even tho one must argue its really "suspiciously covenient" that in first few minutes we several different classes of enemies ... that will be weak enough for us to kill ... yet equipped well enough ... for us to become equipped well enough.

Nope, from story perspective the only thing that actually makes sense ... is that Mind Flayers are mind dominating species, who dont really care what are you wearing, or if there is weapon in your reach ... bcs the main and in some way only thing they really believe is that they will manage to dominate your mind and force you to do whatever they want from you.
Its true that this mindset didnt pay out few times in the past, but thats different story.