Hmm, it's hard to say. I'd say it depends on the proportion, but if most fans produce both, then it's difficult to figure out which factors promote gen fanworks in fans vs. pairing fanworks.

The shoujo (Japanese) fandom I'm most familiar with is Saiunkoku, and from looking at the web pages, mainly gen fans are in the minority, although many people are also interested in the gen aspects as well. But then, it's also not typical because it's a novel.

I have to wonder what the largest current shoujo-based doujin fandom is.