It's a matter of de-cluttering the auto-generated help menu and giving more control to the server admin. Yes, maybe these commands do nothing without permissions for other commands, but if a server admin is giving select permissions maybe they have an argument why a user can only use the standard cuboid selection but not have access to the other shapes available from using //sel. Maybe in another case the server administrator is trying to keep WorldEdit as an admin-only tool, and they don't want new users to see the "useless" WorldEdit commands popping up in the /help and using that as an argument point for why they should have it.

The main argument, though, is that it should be up to the server administrator whether users automatically get these "useless" commands - who's to say they don't have a reason for it?