Sites that have more MySQL Databases created or which have databases that is huge are definitely high end users.
Sites that have large number of databases or huge databases will spike the memory / CPU instantly. This is because when data is accessed in such databases, the entire data is loaded in the memory and hence it spikes the server load. Such spike will affect the functioning of other websites in the server. Moreover such sites will be slower in performance when compared to other sites due to the restriction and resource sharing.
Queries run in the MySQL server will be processed slower than normal rate due to such databases. It is better to upgrade such accounts to a corporate or semi dedicated account where the MySQL is configured to handle such bigger size and frequent access. Such clients will stay with you longer, provided you suggest them the right solution at reasonable cost. Instead of stacking them as one among your shared hosting customer it is good to take this up with the client, he might upgrade to a higher account.
In case of any clarification required for choosing the correct package for upgrade, please contact support by creating a ticket.