That is a hard one to answer to me because it boils down to what you should ‘just do’, there aren’t solid technical reasons why not to use portal areas like crazy. Old standbys you can use are ease of use and usability…. Less areas mean less drill down and confusion to the end user. If your areas have unique permissions, more areas also mean more maintenance. Or you can cite upgrade issues and the desire to streamline your site for ease of upgrading.
I can sympathize, I once saw areas used in lieu of folders for a document library, all you can do is say “No, you just don’t do that!”. Another way to control this is to remove create area rights and setup a process to submit new area requests.