Horses can go through nether portals if i remember correct its just up to the dev to code it correctly.
Any mob can go through nether portals, so having horses in the nether will probably be easy to have, besides /butcher and the fact that horses are 90% useless in the nether Problem is, we have water portals.
It's not a problem with minecraft at all.. why would you even jump to that conclusion?\ It's only the plugin, the plugin can change whether horses can go through.
Like all updates, certain things have been modified in the plug-ins, to correspond to the updates in minecraft. This has been true in ALL minecraft updates, so why should it change now? Everyone needs to sit back and just wait for ECC to update, so these changes can be made. It's all in a matter of time. You will have horses. (I hope!)
HUZZAH!!!! HORSES ON ECC!!!!!! Update: Well great news! Horses will be coming in right away! We just fixed up all the known issues we had seen with them. Main one being breeding. We had no way to block it and there was no plugin out there providing this capability; so instead we wrote it ourselves. Thanks kukelekuuk00 (Our new developer) for doing this. Basically we want to keep horses as rare as possible in ECC's main world; and breeding would simply ruin that. First one to get two horses simply breeds 100s and the market crashes. Thus breeding is disabled. - As well this will prevent users spamming horses to kill ECC's performance. Information on how to obtain horses will be released shortly. http://ecocitycraft.com/forum/threads/ecocitycraft-has-updated-to-1-6-1.58808/
Perhaps possible, if you eliminated one or both. As to removing one or two, I'm not sure.. Both have ups and downs.