1/4" holes are quit small, I've seen pics of people really sawing open their airboxes and I have seen a thread asking where to get a new air box. A couple of 1/4" holes can easily be duct taped restoring the airbox to stock.
When you drill holes, is there still filter material or is filter material needed over the holes ?
Sorry. I thought about it more and it is two 1/2inch holes. No mesh or screen over them. They are on the bottom and I never get any splash back from water there. The air intake on the carb is so (17mm) small going any bigger than that will do you no good. If you install a larger carb then you may need larger holes.
The bigger the holes the louder the scoot gets. No need to over do it.