Leave it out. It will allow any water that comes in to drain right back out.
You could get a tiny bit of water splashing in from underneath (it is only about 3/8" diamater / 0.11 sq in).. but not nearly as much as will come in from above.
At it's location, it will get very little direct spray as it is directly over the swinger. You'll get a lot more spray deflecting off the fenders into the top. (although it is still supprisingly little).
If you desired you could slit the plug horizontally across the side so you have a "flap" that would allow water to run out easily, but block some water from coming in.
Brandon -O||||O-
1998 Honda TRX300EX (330)