Well I guess this can be done without, but SMF might frown upon the fact that the database says mods are installed, while they aren't.
To be more specific, up until recently, SMF2 would try to "fix" mods when being upgraded. But this also had the effect of breaking perfectly working forums (with up to date files) that were simply running the upgrade.php script to upgrade the database format (such as, ahem, beta testers). So it wasn't perfect and now it's pretty much up to the user to make sure they're doing things properly.