I haven't been able to find anything that says wound modifiers affect Matrix actions, and I don't know if it was thought of as self-evident, or if it was just omitted.
So, do wound modifiers affect you when you're in VR? The way it's described, I figured no, unless you're jumped in with a control rig. (So, rigging: yes, deckers: no)
I rationalize it that way because riggers, unlike deckers or technomancers, have to feel what's going on, so the "pilot applies wound modifiers to vehicle tests" rule also applies to jumped-in gunnery.
This'd mean, if you get shot at by standard bullets & gel rounds, then run away to jump into your drone, you'd apply the wound modifiers to any tests you make; however, if you just use standard VR remote control, you would get neither the wound penalties, nor your control rig's benefits.
Is this RAI, or is it easier on riggers to just say your injuries in meatspace don't matter; it's just the drone's physical damage potentially reducing its Handling?