To be honest, what I would do is to make the bullets actual 'objects' and make them collide with the enemies, since you already have the moving bullets, that might not be a lot of extra work. Are the enemy bullets also hitscan? Because I do have the feeling they hit when expected.
And, I also noticed, it's not only the shooting through the floor, I think they see me through the floor as well. They start firing well before I reach the edge of a platform.
I'd be happy to play through it again with your next update!
Btw: Just did another playthrough on a much faster PC and it might be my own increased experience as well, but it plays much more fluently now, jumping seems far more responsive as well. Again, might be me getting used to the game, might be my PC, might be both, but still, wanted to let you know. Fullscreen now works fine as well, whereas it was choppy on the laptop.
A suggestion btw. I can shoot enemies well before they see and/or respond to me, which makes it a lot easier for me. I would let them warp in and activate at the same time, or let them hide behind obstacles if inactive so I can't shoot them yet.