The holes are for quick draw.

I wear boxers and they like to wear out right at the bottom of the crotch on either side of the seam. My girlfriend calls them poop holes.

Also why is it so God damned hard to find knit boxers nowadays? Almost everything at the store is boxer briefs, which I hate because they ride up my leg. And when I do find boxers, half of them are a woven cotton that feels like a plastic tarp.