Once they go limp and are floating and no longer blooming, yes, my wife, (and sometimes me!), will just follow the stem down and pinch it off close to the pot. They will break down and fall off themselves as will the petals of the flower if they are left in. We remove them to prevent them from adding to the waste load in the pond and because it looks better. She'll also pinch or cut off any pads that look bad. Most lillies just constantly grow new pads. You really want the pads to be laying flat on the water. While it "looks" healthy a bunch of pads that push up and rise above the surface is not considered good. At least that is what the man in charge of the Longwood Garden lillies told us which is a world renowned garden who supply many gardens aroudn the world with their hybrid Longwood Lilly.
She also has a 3 ft. pruning device that she uses for any leaves or blooms she can't quite get to.
Craig
Pic one is just a run of the mill lily at Longwood.
Pic two is the lilly pond with their large hybrid Longwood Lilly.