If I delete a user account (with owner access) what happens to all the custom reports and other content that user is author/owner of? And is there any other things that should be taken into consideration before deleting a user with owner access?
When it comes to the limitations - you won’t be able to remove the only Owner in the account, but you can delete any if there is any other user with an Owner role assigned.
Considering the reporting part - if this user created any reports and marked them private (visibility set to Author only) - you won’t be able to see them unless their visibility is changed to All users.
Here’s a detailed overview of the differences between permissions: Permissions for a site or app | Piwik PRO help center