The more I think about it, the more I want the AI to actually have some kind of response to this. It's like someone else said. The AI is a cloud network, redundancy is a thing. I think corruption of the design should affect both AIs just because that's what's actually intuitive... but the AI should also not just sit there and take it. Presumably, when you get the AIP to the point that the AIs get ship unlocks, that's the point where the AI says "Hang on, these guys are actually a threat and what we have isn't working. Let's try something else." So, when a ship flat-out isn't working, why not have the AI respond by just immediately replacing it? This way, the corruption won't really flat-out reduce the amount of ship types the AI has, but you can delete an AI ship type and have it replaced with something else. In this scenario, the AI realizes that "This ship type isn't working anymore. I don't know why. Let's increase security and get another ship out there."
Now I wonder on a different topic as well. If there are redundant backup servers, should we also squash those down to 1? This'd prevent people from copying, then corrupting the design... unless there aren't actually redundant backup servers.