It is correct that if you uninstall a legacy add-on in XF 2.x, this can leave data and database changes behind. The reason for that is because we cannot run any uninstallation code from the add-on because it is written for XF1 and that code cannot be run on XF2. If there are any add-ons that you 100% know you cannot use in XF2 and the data is not important (i.e. it cannot be migrated to another add-on) then it's actually best to uninstall those before upgrading to XF2 if you can.
For any installed add-ons when upgrading to XF2, they will be marked as "Legacy" and can be updated just as any normal add-on if there is a 2.x compatible version.
We'd recommend cleaning up the file system using our add-on.