yes holes, if I remember correctly
Seems like the headliner had to be removed to get to them but I just can't remember Mine was a 99
you will either have to epoxy the holes, put plugs into the holes and seal them, or weld them shut, I don't think the rails look bad at all and do not detract from the looks of the car. But without those rails there is a large expanse of flat (slightly arched metal that can be dented easily.
I never removed mine but I seem to remember looking at how they were attached because there was a problem with mine but I wound up selling the wagon after a few months and never looked at it again.
00 540 sport 6 speed.