no pinholes dont matter. however it does matter where the pinholes are. if they are scattered all over the kite no big deal. However if they are about 3 inches (about 6 cm) from the trailing edge, then throw the kite away. Pinholes that are made there are caused by leaving the kite pumped on the beach flappping in the wind and getting damaged by UV for a few years and the entire fabric is about ready to disintegrate.
a brand new kite should have zero pinholes but it is rip stop so if it's tiny it won't really hurt. what hurts is exactly how these pinholes were created you want to figure that out because it might indicate a problem with how the kite was used.