From what I understand, if a polygon is 'bad' in terms of accepted geometry, the game engine won't render it. A problem not unique to FS2

There is a simple way to fix it, which involves triangulating the offending polygon. Fixes the problem, but incerases the models poly count!!!
Basically, you must have co-planar non concave polygons ...or...in english...
If you could take a sheet of 'virtual glass' and lay it on the polygon, ALL vertices should touch the glass ... This must be true for EVERY polygon
Secondly... if you drew a line from one vertex of a polygon to another vertex, it must NOT go outside the polygon. Must be true for all vertices within a polygon.
You will need to find which polygons are missing, and fix them. The holes should go away!