We left all the windows in, same as Gus.
We run a New Beetle ('02) with the inner metal door panels (not the plastic interior panels) in place and speaker openings sealed with coffee can lids. Our car is still street registered and is parked in the driveway, so we like keeping the rain out. We roll the windows down to race, and back up after we're off the track. We aren't competitive for Class B wins and can't seem to bribe our way into C; so the convenience outweighs the miniscule weight savings/speed increase of deleting windows.
If we ever get in danger of competing for the Class B trophy we'll think about taking the windows out. Best advice I got starting out was to not worry about getting faster until after we made the car reliable. After you can finish the race regularly, then work on getting faster. Of course, if we spend too much more time at home these days we may put Lexan in the rear & rear side windows out of boredom, but don't knock yourself out on things you can upgrade later when you are working on a first build.
We are glad we kept the factory defrost and wipers, too. Decided to do that after reading about people struggling to see at Atlanta in 2017 in the snow, and it paid off at both of our December races (Atlanta '18 and '19).