Just wanted to add a note of thanks on this thread, that I too had this problem, and thanks to @R_J 's help, as well as pointing me here, the change to class.categorycollection.php outlined by @rgp is working for me (and this is in a Vanilla 3.2 installation).
Hopefully there's a fix that gets baked into the regular Vanilla distribution so that I don't have to apply this (admittedly small) fix after each upgrade!
I'm going to leave this information for anyone else who had the same problem I did.
In order to get the counts working again, I had to go in and make some changes to the PHP version in Cpanel.
No need to edit any Vanilla files.