I think it’s all down to usability in the end.. I think MODX can handle it, but do you want a list of 100 contexts in your navigation tree? MySQL might also have a limit somewhere (although from 2.1 on you should be able to use selected other database systems too).
What you also have to realize is that your main index.php is going to be delivering all your pages/resources. 100 sites which each get 5 pageviews an hour means 500 requests to the index.php every hour, or almost 9 per second. If some sites suddenly kick off, that can skyrocket.
Clearing the site cache clears the cache for all contexts iirc, so that will also put a strain on your server when that is being regenerated for 100 contexts (although 2.0.8 improves caching big time).
Just my $0.02 based on some theory and my gut feeling about this system. Haven’t tried it yet.