I think it's a little less of a leap to assume he is weak because they are being hunted and attacked by Gith, not because of some species wide cancer of anything.
He was not alone on the ship -- you pass by several Illithid corpses which appears to have been killed by imps, and there's a second Illithid at the helm who appears in the cut scene where he is killed by the imps as you enter the room.
The cinematic has the mind flayers dead before they reach Baldur’s Gate and before Avernus. It’s possible the gith killed them already but seeing the nautiloid was undamaged up to that point, I think that’s unlikely. The gith probably found their location because they abducted Lae’zel. Not that she’s meant to be important but that just says the mind flayers encountered the gith.
But yes, you could be right. It’s fun to toss out theories.
You're right about the opening cinematic -- it's definitely supposed to invoke a feeling of them being under huge strain and the opposite of flourishing. But I think this is because they are being hunted -- the dragon knights have in my mind likely been pursuing them for some time.
(I also think the reason is less Laessie and more the lament configuration that SH has found)
But the main point I wanted to make is that we see another Mindflayer alive (briefly

) on the helm and that there are several dead ones that appear to have been killed only since they entered hell and got attacked by the devils so we can't really claim the tadpoler is all alone.
I don't really think there's any real reason to assume the helmsman and the tadpoler is the same squiddyboi either but narrative conventions would suggest it is so I'm assuming it anyway.