The junk / spam folders will clear out regularly, not sure of the timeframe. As far as emails in the main inbox these shouldn't be disappearing. Emails will delete from the server when checked by mail programs that is configured to tell the server to delete them however.
In most cases mobile devices will not delete mail on the server but most mail clients on PC and Laptop do have this option. I would suggest that you check the settings of all the devices that you use to access email.