Is there a way? Perhaps.
Darkorb or someone else would have to engineer something mightily difficult. Mysql databases are located elsewhere on the server, out from under the directory space of the user, and in a different permission setting, hence RedHat's lovely quota system can't count that disk space under the user's master quota.
There are some threads about this already on the cpanel forum if you do a search.
I'm sure an enhancement request or two (or a dozen) have been made with this in mind. You might want to check bugzilla....