I'm torn on blocking the holes. My opinion has always been to allow for free air movement vs trying to block anything from getting in. On one hand, you allow dirt, water, etc into the frame...but as long as it can dry, its not a huge issue. The other way...you block that stuff from getting in, but it might get in anyway. Leaves a false sense of security I guess. I know my frame is open to garbage, so at least once a year and after every wheeling trip, I get in there and clean the frame out.
I drilled 1/4" drain holes on each low point of the frame, so every few months I plan on popping the plugs out, wash out the inside, let it dry, re-apply fluid film, and reinstall plugs. It may be overkill but I don't want to go through what I did again.