I pretty much only play on Fractal, and I haven't noticed any lack of horses. I agree with Earthling though that resource distribution is different between Vanilla BTS and FfH - you might see "clumps" of resources that never come up in an unmodded game (copper, for example), but on the other hand I actually prefer the increased randomness. In Vanilla BTS, more or less every civ will have Iron, and I like FfH because that (and other resources) aren't givens for everybody with a decent empire.
Although I've done nothing to confirm this, it would also make sense that there are fewer horses, because eventually there will probably also be nightmares to supply mounted units.