The Eurofighter Canard has some holes on top side. What are these holes for?
They aren't holes they're flush screw heads.
The fasteners have some form of recess for the screwdriving tool, like Phillips or tri-wing or similar, and it depends on the lighting whether or not the recesses are emphasized. In the bottom shot the light source from directly above emphases shadows in the screw head recesses. Visibility also depends on the paint coating and how much the paint fills the screw heads.