Ranking is now organized by a predefined set of genres and some of the older categories (Touhou, Idolmaster...) don't exist anymore. Instead, when going to Nico Nico's ranking chart page, you select a genre, then your tag of choice.
The problem with Touhou is that videos are now disseminated and randomly split into "Animation", "Game" and "Entertainment" genres which makes them harder to classify when observing rankings.
Also, how do you check daily ranking evolution graph of Touhou videos now?
Taking this one ( https://www.nicovideo.jp/ranking_graph/fav/daily/game/sm29631571 ) as an example, it's now tied with the "game" genre and you can't finetune more. It's "game" or nothing for this one. And going there don't yield anything anymore: https://www.nicovideo.jp/ranking_graph/fav/daily/toho/sm29631571?watch_ranking
In my opinion (and that is only my opinion, which is apparently rubbish, as always), I don't think that the loss of the Touhou category is a good thing. There were weekly Touhou ranking videos. How are they going to be made now?
Unless I missed something and you can actually see ranking for a "Touhou" category and I was just too dumb to find it (or didn't look hard enough due to my legendary laziness). Also, I have no idea if this is discussed elsewhere (on 2ch for example) and I have no idea of how Japs reacted to this.