Thank you for playing!
1. Flame, laser, stacked munitions, and smoke all work underwater for some reason. I think that there should either be a diegetic reason for this or the weapons should be disabled (or just not work properly when brought in).
I don't see why these wouldn't work while in water? You're not under the water, you're floating over it, so they should all be just fine.
2. When smoke is deployed, it can't be shot through. At least not with the laser. It's like there's this hitbox blocking projectiles from passing. I think there's the same issue with other grenade types.
This is an issue that'll be fixed in the next build. The system I'm using currently for the smoke clouds basically has them as solid objects, so the laser ends up treating it like a building object. Same thing with the spider mines, it's not great.
3. I also don't know how to use the melee, so... how?
Press the F key or check the settings menu, you should be able to rebind it.
Cheers!