I am also inundated with mushrooms in my tank. If you want to get rid of them you must pull them off the rock and not leave any pieces behind. If any piece is left behind you will soon just have more mushrooms. I cut mine to trade or sell and the "Stumps" grow back and sometimes grow into more than 1 new 'shroom.
If you do just want to cut them, you will have no problem in a large tank. i have cut up to 150 at a time and never had any pollution problems in my 180.