It checks if there are any modules configured to display in the particular area of the site on locations user1 and user2, and if there aren't any it won't put the empty space where they are supposed to be. There was a good example what happens when you don't use this function on www.rsdev.nl
, but they fixed it
Anyway, if you just configure your modules not to show in a specific area you will get empty spaces, if you use mosCountModules() to check if there are any modules to be displayed, you can skip the html stuff that will draw the module 'boxes'. Hope this makes sense.