I actually just noticed something. If you have two of the exact same weapon, you can hotkey them similar to spells (double tap hotkey to dual wield). However, if you smith the two weapons, this same process keeps unbinding the hotkey.
For example: I hotkeyed two steel daggers (fine) to the [1] key, and Firebolt to the [2] key. If I have both daggers equipped, but switch to Firebolt by pressing [2], the two daggers are unbound from the [1] key. I have to go into Favorites and rebind the daggers to [1].
If I do the same thing with unimproved weapons, it works as planned.