I think you put your finger on it. If she has a cold/upper resp thing going on, it can certainly increase her intracranial pressure enough to trigger a headache that may seem to mimic shunt malfunction. If she has no other symptoms, that's probably all it is. Severe congestion can bring on killer headaches for us because they raise ICP in everyone, but since we have a greater sensitivity to it, the consequences are far greater. An annoying headache from such congestion for someone who doesn't have hydro can quickly become one that could kill a horse for us. The immunity system's effort to fight the illness off can also, as you probably know, be exhausting. Add the ICP increase to that, and it's the brain's way of saying, "UGH...I can't work under this pressure
!!" so fatigue and malaise set in. As long as she improves over time and her awareness (when she's awake) is good (i.e. she knows where she is, what day it is, etc), she should be okay.
If she worsens, or other symptoms such as confusion, seizure, or persistent vomiting occur, call the nsg and get her checked out.