Okay, so the idea isn't that they are 'banned' in the sense that they are illegal for tournament use, but they are 'banned' in the sense that it isn't one of the ten standard custom setups that can fit on the WiiU. Back when customs first came out, it was noted how much the custom process could slow down the already process between games at a tournament. For each character, four special moves that each have three possible choices, meaning 3*3*3*3 = 3^4 = 81 different combinations of custom moves. Per character. Only ten custom setups can be saved for a character at any time, so if all 81 combinations were to be 'legal', there was the possibility of needing another 2-3 minutes between each set to erase and set up a different custom configuration, having to erase a previous (potentially popular) custom set for a niche one that's only going to be used once. Compile that with nearly 2000 entrants at EVO, and that spelled a potential issue for TOs and maintaining a schedule with the already known to be slow Smash4 brackets.
In order to help avoid this, the Official Custom Move Set Project came here onto Smashboards and asked each forum to collectively decide upon the ten most likely custom setups for their character, which could then be pre-loaded onto the WiiU before the tournament and avoid even more extra time between matches. Luckily, many characters had one superior option for at least one of their custom specials, and so most of the ten options were based around one or two fundamental moves. Very niche sets, unfortunately, were lost in favour of more 'standard' setups with tweaks in one or two custom moves, and there was little love for most moves considered (by popular opinion) to be inferior to other options (i.e. Interception Arm, Breezy Flight). I hope this answered your question!