Aria does not currently have background encryption threads like InnoDB does.
This means that if you change the value of aria_encrypt_tables, then you need to manually rebuild existing tables with a process like this:
1.) Enable Aria encryption:
2.) Rebuild the table that you want to ensure is encrypted:
3.) Confirm that the table is encrypted. See the following documentation section for that:
I suspect that a table would also have to be manually rebuilt after a key rotation.