As I understand it, the Repair System has been completely overhauled, at least with the addition of Repair Kits that would work similar to Repair Hammers or those Alien Epoxy things from Mothership Zeta.
But it wouldn't make much sense to be able to go over 100% for guns. I guess with swords you could make the blade extra sharp or whatnot, but a factory fresh gun will always shoot the best, unless you actually modify it in some way and that wouldn't be repairing.