as of today (17th June 2018), USB Loaders are allowed in the F-Zero GX ladders.
additional rules have been added to the rules page to reflect this. ( https://fzerocentral.org/viewtopic.php?t=13683 )
there's also a topic for discussing these rules and possible updates in the future ( https://fzerocentral.org/viewtopic.php?t=14221 )