Okay, I"m starting to think this might be a general oversight with any stowaways that don't give flat stat increases. Anything that's supposed to boost your levels doesn't work fine without a shell, but I've also discovered that any stowaways that give you a fish companion still work without a shell. I'm also curious to test if this works with things that give more general bonuses, like the faster attack speed one and the ones that boost your balance damage.
(I'm doing a no-shell challenge run, so this will be good to test if any stowaways will still be useful without one)