Well, it already had been so twisted that if I say "it is female body with either set of cock+balls, cock+vagina or cock+balls+vagina" some comes from somewhere ans says "No shemale is male body!", but to be honest, it was the first time someone said this to me.I think the simple answer is that shemale was never very popular, because it doesn't appeal to straight men (or strictly gay men for that matter), whereas futa became popular because it appeals to straight men*. But the fewer people into shemales are likely more seriously into shemales than most futa-enjoyers, who I think have futa as a side-preference to ordinary straight sex. So when futa started making it's way to the West from Japan, the shemale lovers realised that if they hitched their not so popular fetish to the much more popular futa, they could spread shemales to a much broader audience and divert some of the love for futa towards shemale instead.
And it seems to have worked. Virtually every porn site I know of lump shemales and futa together (despite not at all belonging together and sparking reoccuring complaints and debates such as this one) and half, or maybe even more than half, of everything tagged with or even named futa is actually shemales by this point.
* Straight men is the porn industry's main cash cow.
However about popularity: Yes, I agree, that shemale is not used that much, because shemale on male is not that popular to straight men as a futanari which still has a vagina for men. I guess shemale on female still is ok for many.