I just completed the MKVI mission and sure enough I now have four equipped weapons even though my inventory screen only shows three slots. My question is, can I exploit this bug through the rest of the game? Will I lose the fourth slot if I try to equip different weapons, move guns in and out of my stash, etc? I have paid a lot of points into the ranged skill specializing in pistols and rifles. If I can keep three guns plus a deck I might put some points into shotgun but not if I am going to lose that fourth slot.

Sorry to disappoint you, but if you want to change weapons you have to unequip one first. And then you're back to the regular 3 slots.
So unless you already have the deck and guns you want to use until the endgame, don't invest karma there.

Actually, you can run with all four weapon slots for the rest of the game. The key is to purchase your new weapons from vendors but send the new items to your stash. Don't sell anything you have equipped and don't try to swap in the vendor screen. Then you can go to your stash to make inventory changes. You will find that the fourth "hidden" weapon changes between stash visits. Make sure you quicksave between steps in case something goes wrong.
Once you have your inventory arranged the way you want you can go back and sell the old weapons or decks.
I just beat the game and I kept all four slots from the MKVI mission to the end. I had no trouble upgrading my weapons and decks once I figured out the trick.