If the additional slots aren't locked for the purposes of utilities they will immediately get filled with HRPs, meaning that's an (approximate) extra 400hp and 28% resists for small ships, 200hp and 14% resists (approx) for mediums and large across the board.
I'm generally of the opinion that it's a good idea to add automation, however, quite apart from that is the constant issue of health/TTK bloat in your game which will just be exacerbated by this. Even if they're only size 1s.
IMHO you really, really need to rein in the modular system, particularly with regard to defences because both the discrepancy between stock and engineered ships and the constant hikes in TTK are fully out of hand.
Please consider introducing these new slots (and retroactively restricting existing ones) as "utilities only" or "CPU slots" or something or this bloat will never end.