I installed Better Horses... two months ago? The first thing I noticed was that every horse in the game was suddenly bald (no manes), but after playing around with the mod's features I concluded that it was a worthwhile trade-off and hoped the modder would solve the issue in a future update.

The mod hasn't been updated, appears to have been abandoned, and the most recent official patch has broken most of its functionality. I can't even get horses to gallop anymore (shift key). So I uninstalled the mod, and noticed that horses were still bald. I tried starting a new game, and they were still bald. I tried starting a new game without any mods active at all, and they are still bald.

Has anyone else experienced this issue? Is there any way to fix it without re-installing the game? The thought of finding and installing all those mods again...

http://www.youtube.com/watch?v=ZRY361U3A5Y

Sorry, it had to be done.

Better Horses does not touch the horse meshes (I think), so it should not cause this issue. Do you have other mods that alter horses? Like horse armor or anything like that? Check your meshes\actors\horse (or somewhere around there) and see if you have any horse-altering meshes.

Also, Better Horses (as stated in its Readme too) digs quite deep into the Saves. Did you use it's Uninstaller to uninstall the mod? Even so, I read in the comments that it still makes some horses unplayable for some people. If your saves are already affected, your best bet would be to start a new game, or revert to a save prior to installing Better Horses (with Better Horses removed, of course).

Starting a new game without any mods active will not guarantee a "clean" save. You have to uninstall to get a clean save. That means removing any .bsa or loose files that come with the mod too, not just the .esp.