I too have used quite a few vacuum easels, mainly for exposing film, but also for fibre based paper, really keeps things dead flat.
Masonite makes a good base material as it is pressed flat, fine sanding after drilling will flatten the imperfections.
I agree with Drew, much smaller holes and lots more of them, very much like Steve Roberts posted. I would suggest you entertain the thought of using 2mm or 2.5mm sized holes. You could try 2mm first then if not right, enlarge them to 2.5mm.
A series of masks to close off the unused holes will also greatly help, or use removable painters tape tape to block the unused holes.
Mick.