yes there is, they solved it by simply making you unable to repair unique weapons with other weapons, thus they never appear in the repair menus, uniques can only be repaired with repair kits or at vendors.
Not true, they simply ported over a system from FO3's DLC. If you remember, the DLC uniques didn't appear in the base forms' repair lists, but you could still repair THEM with base forms. But there was never a chance that you could destroy your unique since you couldn't use it to repair anything else.
You'll still be able to repair "Maria" with regular 9mm pistols, and the "All American" can till be fixed with regular Marksman Carbines. You just won't be able to do it the other way around.