Originally posted by Gargoyle Girl:

I'm not saying I know how to program it, but it seems like they would need to add some code to certain items that allows smoke particles or projectiles to pass through.

I assume the problem there is they're using a third party physics engine that doesn't support the idea of an object having a hitbox for one entity while being immaterial to another. I can imagine a dozen ways to work around that but with a lot of potential for release day Skyrim grade bugs.