It's not every year that a Special Reitaisai event (SP, Autumn) is held, in these cases, it isn't every circle that is willing to take part in every single event. Last year's Autumn Reitaisai had ~1200 circles, let's say about 500 of them couldn't make it to Reitaisai 11 and decided to participate in the next one (which would be Reitaisai 12, but it ended up being the Autumn one instead) and not all of these circles are too skillful or at least experienced to be attending every convention with new material. So basically, there are circles which attended to Autumn Reitaisai and won't be in Reitaisai 12 as participating circles, otherwise I believe the numbers of the next Reitaisai would be around ~4400 (and besides that, there are other Touhou events during the whole year)
2 years between Ten Desires and DDC, and now almost 2 years between DDC and a spin-off game. ZUN got married and had a child. It's pretty normal that the numbers would go down a bit, I mean, fighting games are cool and all but the official non-spinoff games usually bring us an entire new character cast and new plot (useful for manga circles) and new music (for the music circles). The lack of new official material is what causes doujin circles numbers decrease. For instance, Kuroko no Basket had 400-600 circles for a while, when a new anime season aired, it skyrocketed to ~1400.
If you analyze Kancolle's numbers before the anime, it was pretty much constant. The game was always popular to be honest, a free browser game that's easy to play, of course it would be pretty known. And now, Kancolle is going through it's peak with the anime, but it seems to be slowing down a bit already, few months ago it was viral on niconico, but a few weeks ago, a Touhou video reached top 1 ranking again with overwhelming 300.000 views or something. While the most recent Kancolle video had only 100k and didn't even reach the top spot. The game is supposed to be how it is now, a simple game that everyone could play easily, meaning it can't really expand it's grounds to another platforms, otherwise it would lose it's very purpose. It's way easier to create things based on a game that gets updated constantly than on one that gets released in a margin of 1-2 years. Of course we, Touhou fans, have the mangas, but it's very little material compared to an entire game.
Believe it or not, one of the main reasons Touhou peaked at ~2011 was the anime created by manpuku jinja, it was successful enough to get four episodes despite it being fanmade. Japanese people love anime, that's why animations there in Japan cause the original source of a series (Light Novels and Mangas) to sell a lot if they're well made. While Kancolle had help to reach the peak with an official anime, Touhou was the same with a FAN animation, furthermore, I'm pretty sure that Kancolle's anime was made to please the fans and make the game more known, so it won't be getting fanmade animations (it has an official one already, questionably someone would want to do another). On the other hand, Touhou is getting a new one soon, if that "Hifuu Club Activity Record" project goes well (and it seems to be doing really fine), it surely will be something.
Okay, enough with the anime talk. Reminder that there will be Touhou doujin games in PS4 and Vita, and for some reason Japan loves Playstation a lot, meaning that if these games succeed, they will be really popular. Besides the console fangames, there will be the fighting game soon and hopefully Touhou 15 not that far from us.
And If I remember correctly, Touhou is getting a western release soon. The NHK interview was really suspicious, but the written script seemed to be reliable, and even without that, it was a bit obvious that ZUN would like to release his games here in the West too, afterall he experimented putting one of his works on a digital platform.
Touhou is well known outside Japan and it's getting more recognition here outside Japan to be fair. But regarding the numbers slight decreasing, it's because these cool things I stated above are still being done. Other series logic can be applied to Touhou too, if Touhou things weren't being valued at all, than I may would say that it's dying. But seriously, if even Startrek could reach an stable level on it's fanbase, how could not Touhou do the same? And by the way, with Touhou getting released here, it will get a lot more recognition than dumb speculations about it dying (like how it mainly was last year).
Just needed to spit it out, obviously with a bit of slow down from ZUN we would slow down too, and with his projects coming back to it's pace, we will just follow it. That's how the majority of the fanbases work after all.