I'll preface this by saying I'm not on Riot's esports team, nor do I work for an esports org. I'm just a fan who notices some things.
Nautilus probably isn't picked more often for a few reasons. For one, he gets bullied pretty hard by the current power picks. When so many current top laners bring both teamfighting and lane pressure (Shen, Gnar, Ekko), he's not really gonna do much. The fact that tank items are really wonky for him right now doesn't help either. I guess he could also be played support, but basically every other melee support brings something so much better than Nautilus, especially Braum.
Vayne isn't picked for two reasons. First, if you want early game, she's completely worthless and you should never pick her. If you're looking for late game, then why not just pick Sivir? She does basically the same damage late game, and isn't shackled by her requirement to be a dueling ADC, which is basically a contradiction in pro play. BoRK nerfs from a while back didn't help either.
Yorick is disabled for Worlds because they disable new champs and reworks right after their release, in case they're broken beyond belief. Since Worlds is a weird case and they want to keep things even throughout the tournament, they're just gonna leave Yorick disabled, since nobody was gonna use old Yorick and it's safer and easier just to keep new Yorick away.