I am using the latest version - I created some forms, added some test data to it, then I went and deleted the entries and reset the counter back to 1.
In the database table for the form, it is completely empty. On the forms I was testing, I had a field to upload files. When looking at the /files folder after fully deleting the entries, the files were still there.
To me, if you are fully deleting the entries, it should also delete any uploaded files associated with those entries.