Yeah, gun damage isn't very important but I still shoot at enemies all the time anyway. It's gotta help some, right? Tags is where it's at for real damage. Keep in mind that you can only tag one enemy a certain amount of times, more than that is only useful when fighting multiple enemies at the same time.
I don't know if I have all the guns, but here goes nothing. Cerberus, the first, is useless after you get another gun of course. Mizuchi didn't get much use from me, it seemed troublesome. The one you mention must be Naga, or at least I never got one called Hydra. In any case, Naga is good until you get Orochi, which auto-fires in seven directions with every shot and allows 8 tags. I never liked using Technos since its two-way shot seemed useless except in specific situations that I never found myself in, and it allows only two tags. Vasuki is the one I use the most because it's got a homing shot that lets you tag enemies you're not even aiming at, as long as you hit a target with your first shot. This is very useful, except for when you need more precision or want to avoid hitting a certain enemy (one particular boss fight is a real pain in the butt with this gun). Vasuki lets you tag 4 times, and that's enough for me. Then there's Dullahan, which turns the whole thing into a more traditional Mega Man-esque game, with no tags and actual shot damage that's worth something.
Have you been making accessories? Get the Boost Band ring (preferably the "plus" version) as soon as you can if you want to double jump. If you think Prevasion (that thing that lets you avoid damage if you're not attacking) makes the game too easy, simply unequip the Prevasion Chain.
