They do not necessarily disappear in the mounted phenotype. You just need to port the cloak to theta phono too.
Interesting.
Bioware intentionally disabled cloaks and shields in the normal mounted phenotype. However, thanks to your insight, I now see that they only removed the shield node, not the cloak node; they just didn't make the cloak models for riding.
I find, though, that even something as simple as a hat looks completely wrong when renamed for the mounted phenotype. I'm not sure whether you've remodelled the hats, or moved the cloak node?
At any rate, hoping that the Community VFX project will do more on this, I've parked the issue for now.