Well, it still keeps dust from entering your sensor chamber, and if your camera is cooled it stops (to a certain degree) moist air from producing ice on your sensor and electronics. But apart from that, optically it should not have much effect, only slightly increasing the backfocus.
I kind of ruined the IR window of my 178MC (long embarassing story) and since I already have a 178MM and am waiting for the LRGB filter set, I figured I could just use the L for both cameras and save some money.