On systems unfortunate enough, full screen mode can be dangerous unless the graphics plugin is properly configured for the right resolution and refresh rate. If one can find the configuration for these settings, that person can find the configuration to enter full screen manually as well as set it to happen the moment a ROM is loaded. Most people are used to the whole Alt+Enter shortcut to do the trick, anyway, for those other programs. I think it is already obvious enough how to manually enter full screen.
Besides, making it run in window mode adds the uniqueness to emulating the game instead of playing it on the actual N64, and it also allows for opening GameShark cheats and other menu commands. For these reasons, windowed mode on default seems much better and safer.