I personally use second gun to apply status effects, having different weapons for different enemies isn't working out that great so far.
Sorting and combine all sound reasonable, I'll probably implement them later.
Yeah, balance is a big issue. Right now it's too easy to just use a weapon that floods the screen with bullets, it become even easier compared to the previous version, cause minelayers' mines are no longer triggered by shots. I was going to add an enemy that reflects your bullets back at you, but it's turning out to be harder than expected. As for rarer modifiers, it's also a problem, cause you want to make them unusual, and leave boring +damage, +firerate, etc. for more common ones, but in the end it makes them more situational, while basic mods reliably boost your damage output.
And yes, you can make something broken using them, e.g: stacking Exp after Exp increases the amount of shrapnel exponentially, and can create a gun that deals thousand of damage with a single shot. Or putting Ho after Tra, which creates a gun that shoots bullets that shoot homing missiles...
I'm planning to make the game harder by tweaking existing enemies and introducing new ones, but balancing that is gonna be hard. And as I've said in the comment to your game, I don't like the idea of just increasing the enemy hp.
Anyway, thanks for a detailed comment.