If you're looking at horse mods, you might want to check out http://www.tesnexus.com/downloads/file.php?id=16688. It makes Slof's Horses 2 compatible with a bunch of stuff and also puts armour on the Imperial Horses. It solved a lot of my horse mod compatibility issues. Ulrim is back on the modding scene, so any issues might get addressed, although I didn't have any problems.
I believe it's actually Guard_Names.csv under Import Names in Wrye Bash that results in this behavior. I don't use rational names myself, but have similar types of horse names since checking Guard_Names.csv to get more unique names for the various guards as well as horses. Wrye documentation says "A names patcher file that covers guards, legion soldiers, couriers, and a few other generically named characters and creatures from both Oblivion and Oscuro's Oblivion Overhaul. ; * This is based on Flak's Complete Names Project. However, ranks have been strongly tweaked from Flak's version and OOO names have been added." Looking at the documentation for Flak's mod: "This mod aims to replace all those npcs and horses with generic names, and gives them a unique, semi-lore correct name to identify them by."
So, working as designed if you use that option.