I spent quite a few
hoursminutes making this based on what phflack said and then realized you mentioned the bricks show up 2 times in the menu, which means there are no actual conflicts and you didn't actually need a uiName / database conflict checker.
It might still be doable though, but just to clarify before I do something else that's pointless, you are talking about just regular bricks, like prisms, plates and so on? Not special bricks, that is. In that case instead of checking .cs files you'd be checking each .blb file for the file to be a BRICK and then compare the sizes which would be even worse but still doable.
Done that as well anyway: Searches every single .blb to have the second line "BRICK", puts stuff in array and then compares for standard dimensions and flipped dimensions, since they'd still be identical.
I can't really test this too much as I don't use BRICK Add-Ons but I made some test cases and it worked fine.
I'm including both in the .zip because why not.
You need to have Python installed (they are .py scripts), place & run them in your Add-Ons folder.
http://leetlegacy.tk/files/blocklandBrickCheckers.zipbrickCheck.py checks for identical BRICK files.
conflictCheck.py checks for uiName / datablock conflicts. This will reveal missing bricks, not duplicate bricks, as these conflicts will prevent the brick from even showing in the brick menu.