The WiP version of Wrye Bash (or *A* WiP version, perhaps...) can do it, sure. The "Rel" version, however? Nope. At least, not as far as I'm aware.
I suspect most use OBMM for it, or just copy/paste "by hand", given that they're pretty much a different kind of thing (to textures, meshes, etc.)
edit: Oops. Well, I'm not sure if even any WiP version of WB can do
Oblivion shader file edits. But you can use it to install ".fx" files, for example. So, yes but also maybe no. :shrug:
Probably no, I'd say, at this stage at the very least. If not, I really wish it could be added in...