Aria does not currently have background encryption threads like InnoDB does.

https://mariadb.com/kb/en/library/innodb-background-encryption-threads/

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:

https://mariadb.com/kb/en/library/aria-enabling-encryption/#encrypting-existing-tables

e.g.:

1.) Enable Aria encryption:

MariaDB [(none)]> SET GLOBAL aria_encrypt_tables=ON;

Query OK, 0 rows affected (0.000 sec)

2.) Rebuild the table that you want to ensure is encrypted:

MariaDB [(none)]> ALTER TABLE mysql.global_priv ENGINE=Aria;

Query OK, 7 rows affected (0.017 sec)

Records: 7  Duplicates: 0  Warnings: 0

3.) Confirm that the table is encrypted. See the following documentation section for that:

https://mariadb.com/kb/en/library/aria-encryption-overview/#determining-whether-a-table-is-encrypted

e.g.:

$ sudo strings /var/lib/mysql/mysql/global_priv.MAD | grep "root"

I suspect that a table would also have to be manually rebuilt after a key rotation.