Oh, yeah, EMP makes a lot of sense, flavor-wise. Brilliant idea! Different ships is also a cool idea, presumably with different attack patterns. Wouldn't really work if there's just one variant ship, but having the juice unlock those could work, if you don't want to do upgrades. Wouldn't exactly work flavor-wise, though. I guess... if the juice is used to fuel some sort of alien generator or whatnot, the energy from that could be used to construct the ship?
The captured pilots having a hidden transformation time alongside their resource production times definitely should be un-hidden in some way. You probably don't need to make a timer shown for each individual pilot, that feels a bit overcomplicated and would probably clutter the screen, but having two counters for "transformed" and "untransformed" pilots would work, IMO.
The thing about the pilots having their own choices is interesting, although I feel like it could diminish from the actual gameplay, especially if the reason is only explained later in game or something like that. Since I imagine 99% of people playing this assume you're hypnotizing and enslaving the pilots, like you'd expect from the hypno genre (and the term "captured pilots"). Maybe during the end-of-round results screen, you could mark one job as "recommended", so you'd get more captured pilots choosing that role? Or, if you get some aspect of control over it. Like, if there were 3 main "rooms" that the captured pilots choose randomly between, but there were sub-jobs within those "rooms" that you could choose. Like, there could be a "production room" with milk and cores, and a "support" room, where you could put people to... IDK, speed up transformation time or something? That's probably way too complicated, though.