I have designed my own date picker in a button popover. It is used for setting the completion date for a task. If the task is incomplete, the button's hover state works fine. If the task is marked complete (by selecting a date in the popover), the button changes color to green if the task was completed on time and red if it was completed late.
When the task is complete and conditional formatting is applied, the icon's hover state no longer works although the button still does exactly the same thing: open the popover. I'm not sure if I see this as a bug necessarily, but I find it problematic. All of the clickable buttons in my solution hover. The user knows that when a button changes color as he or she rolls over it, the button may be clicked. If I use conditional formatting to offer visual cues to my users as I described above, I lose the consistent hover.
The only time I can see not wanting to hover (and I have some buttons like this) is if conditional formatting is used to gray out the icon and the script that runs simply exits because it knows that the icon is grayed out.
In my opinion, by default, conditional formatting should only be applied to the normal/active state and hover should always work. I would like an additional checkbox that says something like "Apply to all Icon States". If the additional checkbox is checked, then the formatting applies to all icon states.
Conditional formatting on text and fields should work the same way in my opinion. It's just illogical to assume that because one uses conditional formatting to change color, one no longer wants the hover effect to work.