No, it's not ruined forever. It is kinda annoying how hard those hats are to get. The bonuses should apply to just the weapons together, or better yet, not at all. It's adding an unnessecary layer that's hard to read.
If you see a sniper with the rifle, shield and hat, you'd assume he can't be headshotted. He might not have his melee though, and you're not going to see it to make that decision. Similar problems exist with the other sets, they're too hard to read.
If they were going with bonuses, I'd have 'em like this:
Equip the Powerjack, get the speed boost and damage taken increased.
Equipping the Degreaser over the flamethrower has no real disadvantage. Not that that's a bad thing, it's exactly the kind of skill based buff the Pyro needs. The whole disadvantage of the set bonus is giving up your insta kill axe. Giving the bonus just to the power jack would remove the complications there.
Remove the scout's bonus completely.
It's unnessecary. Everything is balanced as is with the new kit.
They need a more interesting bonus, and one that has a downside at that.
Have the soldier's sentry resistance tied to the Black box.
It's the lack of rockets that hurts when dealing with sentries, not your shotgun. It's easy to see when he has his secondary equipped though, so I don't mind this one.
Have the spy's bonus tied to the set without the hat.
readability doesn't apply to the spy; misdirection is more or less how you use him effectively, so having it being a full set is okay in this case, sans hat of course.
Remove the sniper's bonus, and his weapons.
They're absoluely terrible. Except the knife. That one's okay.
The can't headshot/can't be headshotted thing is incredibly stupid. The absolute worst idea I've seen for the sniper in fact. I expected a lot better than that. Hell, anything would have been better than that.
The shield is like the razorback, only worse.