I haven't really seen much on this issue, and even less fixes for it. For all I know it doesn't even have to be cliff racers, although I have yet to successfully duplicate this problem with any other creatures/npcs. The problem is this: sudden drop in fps that is solved by toggling collision. Some people have reported this for clutter and statics, but I am reporting it for cliff racers. Basically I was wandering around the ashlands and got a massive fps hit once I loaded Assarnatanat's cell. ( http://www.uesp.net/wiki/Morrowind:Assarnatamat ) It seemed understandable as there are a lot of statics plus something like 20 actors on the scene (modified spawns using WAC and vanilla Oblivion). So I thought I probably overdid it. When I got close enough to load the actors my fps was about 3 and I had to tgm and type kill on everything, but afterwards my fps didn't increase by much until a random cliff racer attacked me out of nowhere and I typed /kill on it. I knew it wasn't consistent to just have a typical cliff racer in a cell cause lag, so I decided to investigate and came across the tcl to fix lag issues and cliff racer related lag threads. Luckily I had saved right after loading Assaranatanat's cell and found that some cliff racer spawns seem to place them in spots where they easily get stuck.
There are two cliff racers stuck in the structures, and I've seen a third. This doesn't happen all of the time. Sometimes (if they even spawn) they are outside, although in this particular location it seems like there's consistently one that is stuck. However, they don't really cause problems simply by being trapped. In order to duplicate this issue they have to be stuck in a mesh/terrain, which isn't actually hard for creatures to do, especially the racers it seems. I played around with this for a bit and found a hard example (unfortunately I assumed my fps counter was enabled for screenshots, but with all actors dead the max would be about 10 with the racers causing problems, less depending on the rendering).
The racer with the wing stuck in the wall is the problem, and in this instance toggling collision increased my fps by around 15 (25-30~ total). So, reloading to find a stuck cliff racer again, I found that typing tcl on a problem (stuck) racer will also nullify the issue. This only works if it is alive. Untargetted, tcl will not work on live cliff racers, only dead ones. I found yet another example with two dead cliff racers right on top of each other that would also cause the fps drop. The instances when they are dead and stuck are unfortunate, as I don't think you can move them (at least I can never seem to drag their corpses anywhere, even if they are only on top of each other), which results in that cell being a problem until the corpses go away. Typing a non targetted tcl will fix it, but there are other issues that go along with that, especially when it's an entire cell to be avoided. At the moment I don't know how to fix this issue. Since they don't really fly anyway, for now I've ticked walks and swims along with flies to see if that will help them to not get stuck on things so often, although I don't think it will. I know nothing about meshes so the only other thing I can think of is to replace the racers with another creature. That would be unfortunate, but depending on the number of times this happens it might be worth it to some people. I've read something about a creature revision underway, and I found a thread by Hashmi1 with cliff racers being worked on, but the files have been deleted and I assume that they have already been incorporated into the support files, which are the ones I am currently working with.

#1
Personally I think that the problem has more to do with PathGriding and Placement ... but anyways here is a little tweak that you can try:
Step 1) Delete the folder (data\meshes\creatures\cliffracer\)
Step 2) Download and copy this to your Data folder.
Step 3) Open the CS and change the cliffracer's movement type from "Flies" to "Walks" ... save as an esp and load the game with this new esp {you want to UNCHECK flies and check walks}.