Can't you put 2 proton bomb cards (or any bomb) to one bomber?

Because neither of the squad builders let you do that, and I don't see why not.

The same with missiles.

The rules reference notes that you can't equip 2 of the same card anymore.

That is what the RR states... kinda flies in the face of what purpose of a bomber is, BUT with the automatic damage those bombs can do now, its probably a balance issue.