That's not unheard-of when you have a relatively thin piece of aluminum trying to resist hundreds of pounds of tension. I have some wheels built with Weinmann single-wall rims that have a couple of slightly pooched-out spoke holes. I'm not sure if they were like that when I got them already well-used, or became that way during the 17,000 miles I've ridden them.

I would happily use those rims, and using nipple washers, double-butted spokes, and moderate tensions would greatly increase the chances of long-term success.