As far as I can say all guns act different and not as upgrades (maybe except the flamethrower over the incerator).
I recently only discovered that there is a railgun for your main slot. So I've still haven't seen them all.
There is the main machine gun, the hornet nest that has a faster attack speed (but lower fire power and bigger spread), the grenade launcher, flamethrower, railgun (sniper-like weapon), I found today for the first time a tazer that travels through walls andere there was another weapon where I forgotten the name. Main weapons aren't many tehre because they have infinite ammunition and it's hard to balance this stuff right.
There are more secondary weapons like guard blaster, combat shield, rainmaker, shotgun, boomerang needles, phase blaster, different types of mines, poison stuff, flaming stuff. Then there are the drones, the modules and th econsumables. And you can all combine it like you want, giving you even more possibilities.