As far as I know, MySQL usage isn’t tracked by itself. MySQL usage suspension are not based on hitting a daily limit, but because the server was actually overloaded and your account was responsible for it.
So increasing the MySQL limits is done by performance tuning on the database server and just adding more server capacity. Which is something that’s also been done recently.
I just checked and it seems that nowadays MySQL suspensions are really rare. So you definitely shouldn’t worry about MySQL usage unless you’re doing something really stupid with the database.
Just to state clearly, nowadays MySQL suspensions rarely happen. In the past, they happened more often, but due to server upgrades and improvements they have hardly happened in the last few months.