Is it true that ZUN once said Touhou and Kantai Collection can go well together? As in a crossover between those two is something he thinks is a good idea?
Short answer:
He said that on twitter, with a sarcastic "w" ("lol") at the end. It was entirely in jest.
Long answer (because this was well-documented):
During and after 2013's 大⑨州東方祭 "Dai Kyushu Touhou Sai" (held on Sep 22), some circles at the convention came under fire for selling KanColle doujinshi at a Touhou convention. While it's common for circles to sell non-Touhou doujinshi on the side, it was said that the only
new works they brought to the con were for KanColle, and all Touhou doujinshi they had were old ones.
As the quarrel continued on twitter, some guys jumped out to call themselves the "Touhou Police", claiming they would purge all artists that betrayed Touhou for KanColle.
On Sep 24 (the day before he left for Atlanta), ZUN seemed to have vaguely heard of there being some argument about Touhou and KanColle. He tweeted:
ZUN: What? I heard there's some sort of antagonism between Touhou and KanColle? Well, I may just up and do a collaboration, make some warship character lol
ZUN: Not really, this will get in the way with my work with Kadokawa (laugh)
ZUN: |-`).。oO( But I think KanColle goes well with Touhou. You should be cooperative in your fan works~
Eternal Touhou: I think some might get the wrong idea that Touhou is indoctrinating otaku into the right wing through proselytizing Shintoism. What do you think about it?
ZUN: I wouldn't reject them even if they have misunderstandings. That's what Touhou is: true freedom is a cruel thing. [Referring to the Touhou ideal: freedom for creation and interpretation.]
ZUN: All in all, the most important thing is, don't quarrel with other fandoms. You can quarrel inside the Touhou fandom however you want.
ZUN: Speaking of warships, the only warship I'm familiar with is Spaceship Gomera [aka "Bio-Ship Paladin", a 1990 side-scrolling shooter by UPL].
Note: Eternal Touhou is the most obnoxious troll in the Japanese twitter Touhou fandom, and might have come up with the "Touhou Police" idea. They would later become a KanColle fan, change their twitter name to "Eternal KanKan", and keep on being a troll.
As you can see, ZUN just wanted to say "you should be nice to other fandoms", but he both displayed no real understanding of the problem, and chose to speak in the most sardonic way he can think of. His friends were immediately like "hey, you shouldn't say that", but that's too late. ZUN had given people the excuse they needed to escalate a small quarrel into a fandom slugfest.
Thankfully, soon they would see the enthusiasm of American Touhou fans displayed at Atlanta, and say, "what have we done?"
At least we get this Touhou Police T-shirt out of it:
