I respectfully disagree-- I don't think the drain is a "p.o." mod -- my 2000 C380 also has the exact same small drain grate molded into the fiberglass "sole/deck/floor/pan" in the forward port corner of the main head compartment. While I have not (yet) traced its path and ultimate destination, it appears to exist simply to catch and dispose of any water that might end up on that section of "floor" from folks using the adjoining separately-drained shower compartment and then dripping as they exit to towel off, and/or splashing, ambitiously brushing teeth, washing hands, pumping/cleaning head, etc., in the main head compartment. In other words, I believe it's really just a built-in design feature intended as a "housekeeping" amenity to try and keep the otherwise-water-tight molded-in fiberglass pan/floor a little bit drier from day to day. Without it, you would potentially have an "above-floor bilge"/cesspool.
And I very much like Peggie's tip about using C.P. to clean/deodorize it--I'm going to do it on my boat the next time I am there. Given my description above, my guess is that it may be a source/culprit for persistent lingering, mystery boat odors.
Cheers.