In SR3, Shitface's Weapon Re-Balance Mod removes these upgrades. I think they either should be removed in this mod too or be made optional (those are already part of an existing mod, anyway). Those upgrades make the player too overpowered (which is probably one of the reasons why there were removed in SR4).
It is optional. You could easily remove those lines of code from unlockables.xtbl, or don't select them in the phone menu if you don't want. Up to you.
On the whole though, Fan of Saints and Shitface have come up with the goods again. Well done guys, and I'm glad to contribute in a small way. Thing is, this is only version 1 so can't wait for what's in V2!