Logic, realism, and other secondary issues aside, the main point of design corruption is for the player to be able to say "you know what, I'm sick of (ship type x), and I don't want to see it anymore". So having it blank it out for both players seems appropriate.
Conversely, there should only be one design storage per unit type, so you can't hack it, then corrupt it.
On a tangential subject, I've love to see a "corrupted design" unit that looks like a train wreck and has no stats--pea shooter gun, no real HP, no armor, no special abilities, etc. that effectively replaces whatever unit you corrupted. The AI would still reinforce with this unit and use it in waves, and so on, as if the AI wasn't aware that the design got corrupted.
It would never use it in exos, which I think are the only ... way the AI has to "pay resource points" in order to send powerful/many units with, so that would avoid the "but how much is it worth, FP wise? Does this mean the AI is going to throw like 800 of them at me instead of its usual 200 fighters?" kind of deal.
At higher difficulties the AI would recognize the error and stop using the ship after some duration, on 10 it would see the error immediately and never reinforce with it.