Nah.. horses aren't missing. I'm sorry if you had them and they're gone now, but because of a bug with them, they breed on their own, and uncontrollably. I've killed off about 1400 horses already, though I can only do it to loaded chunks. Due to their excessive self-breeding, they're causing the server lag.

With our server's ability to TP around, horses aren't that vital for travelling. I think most people have them just for the sake of collection and another food supply. Horse meat.. you sick people. At least make glue, too. So anyway.. yes. I have been killing them off in mass numbers.

It is possible for them to over-breed to the point of destroying the world and us having to reset the map. I have had this issue happen before with cows, they were self-breeding and my world exploded with cows, it was completely non-recoverable. So hopefully one of the coming patches will fix this problem. Because even the baby/new-borns are getting pregnant, so it's snowballing out of control. And at this point, the rate at which they'll multiply in numbers is getting larger and larger. I'm already finding 40+ of them at a time in a single location.