Morrowind does not seem to be able to handle .nif files with no objects in them correctly. I've been using such meshes on occasion, and they have the habit of producing some nasty errors simply because they do not have correct position values in the game engine.
As an example, I used to assign empty meshes to activators which I would place in the game world from a script and have them cast a spell on the player or an NPC. This always produced the following error:
Scale parameters for Magic Effect [...] are bad.
Another common problem was when I tried to return or alter the position of an object with an empty mesh assigned to it, it would sometimes crash the game.
The same problems occur with meshes that only have a single vertex in them. In my experience, you need at least one polygon in a mesh to avoid similar issues.
So what's the solution? Use a mesh that has one simple object in it which is hidden and has no collision. You can alter those flags easily in NifSkope.