I have started tweaking Shells.zon and it seems that it have an effect on power of the Deck Gun (I still don't get why the power of it was changed if Super Gun Mod does not change that file at all, but whatever).
My personal experiences with tweaking shells.zon is that you have to completely go out of the game, otherwise the changes will have no effect at all (usually it works if you just go to the main menu, then spawn in the port (start of the patrol)).
We live, we learn...
PS: I would still like to know how the power of the Deck Gun cha... oh well, you've got the idea