Does having data pruning enabled effect data on a database that is not from historized tags? This would be tables coming from transaction groups and SQL queries.
No. You could just run a scheduled task on those to delete records older than a set number of days. If you check your database you'll find that there is only one table for the transaction group and no partitioning - unless you've done something complicated!
Transaction groups have a "pruning option" built-in.