The ships are designed for four people, you're right. And having less than optimal crew members would also very much mess with balance, as going from 4 crew to 3 means you either have 1/2 your healing power or 1/2 your attack power at any given time, but as it's adventure mode, I think the balance can be messed with a bit to give new options to the players to how they go about adventuring.
Yeah, I'm definitely not saying people should opt for soloing, or even duoing, but I think that doing something like working a goldfish with 3 crew members would be a fun challenge without having the 4th slot filled by an AI. You're still lacking the 4th person, but you do have all the roles covered, so your gunner or pilot doesn't have to jump off their post as soon as the enemy shoots back
A lot of how viable this idea is comes down to how the crew-matching works and how the ai director works.
In regards to crew matching, if it's similar to how match-making works in skirmish mode, then we don't have much choice in the matter. On the other hand, if captains are given a base payment of money, reputation or some type of currency, and they have to negotiate prices with their crew, it could add a very important choice into the mix.
In regards to the AI director, if it's as hard as a lot of the players are in skirmish and goes all out, then yeah, it will blow you out of the sky without a second thought if you don't have full crew. If it goes easier on you for certain missions (think fighting starving peasants turned raiders vs royal navy special forces), then you could try it for whatever difficulty you feel comfortable with.