What will she do?
I'm anticipating:
weigh
check teeth (and hopefully back teeth if they are amenable)
check fur and skin for unwanted pests
check their (beautifully cut) nails
eyes'n'ears
listen to their breathing
their boar bits 
ask about their general health and diet.
They are having a check-up because they are going on holiday in a few weeks and the Rescue recommends they have a Guinea-Pig MOT.
Anything else I need to consider? I will have a serious chat with them about Not Sitting on your Brother's Head (Yes GP1, I mean you )