Custom tables would not be invoked in the deletion process until and unless explicitly referred from the service or component calling any data . Just like when you make a content check-in , until and unless the custom filters / component does not fire the insert statements there will not be any entries made .
Tables like Workflow History need to persist these content items as its purpose is totally different. If a admin wants to know how many content went through a particular workflow, this is the table he could refer to and also know who approved them. It is up to you to truncate records in these tables depending upon the organization need. You can for example truncate records older than 5 years from these tables.