Hey guys- We are currently using the native local Derby database for GOAnywhere MFT. If we migrate to an Oracle or SQLServer instance, will the job logs be stored in tables or will they remain as log files on the local system?

It depends ...

Job logs are originally created and utilized within your database. This makes them researchable. So, if you move it to Oracle, they will go with them. Additional logs (System, etc) are kept in the default logs folder location. When the archive point is reached, then logs can be written to your default log location in an archive folder, if desired.