Here's how to get to it. On the first level, keeping playing until your contact gives you the key card. Keep going until you get to the lift to level 2. Not far into level 2, you'll cross the walkways that hang over a huge pit of crap. Follow them into a room with 3 pipes with flames coming out of them and right after that room is a room where you have to activate an energy bridge (screenie 1 is the area I'm talking about). After you activate the bridge, a small floating platform with an enemy on it will come, quickly kill the guard and jump onto the platform (but destroy that fan FIRST). You need to do this part quick as sometimes that platform doesn't always come back (possible bug). Check the first screen shot, I recommend you stand in front of where I've marked to kill the guard, then step backwards onto the mark and jump when the platform stops. In the second screen shot you'll see a few barrels blocking the way but they can be shot off the platform safely though I have blown them up before so be careful there. Go into the room in the third screenshot and you'll find the grenade launcher in the furthermost crate. The other one has 2 clips for your grenade launcher and 3 for your shottie, yum!!
You can find the grenade launcher in a few other levels too but because I always pick it up here, I don't remember where they were. I know your already past this point but at least you'll know for next time. Still, I hope it helps regardless :)
Regarding the shottie, you are shooting it while crouching right? The shottie is an absolute pain to use while standing but I do recall talking down Thermatrons with it without too much hassle. I crouched and rolled from cover to fire then roll back when the Thermatron prepares to shoot.