I used to have two, well technically there are two (and there were the ones, factory, for the luggage rack.
One I re-used for putting a GPS antenna in, used a brass ring/nut with an o-ring and a cap to seal it (drilled a hole in the cap for the wire. Sealed it up, and put a shark fine over it. The other hole I re-used for a CB/Ham radio setup with one of those Motorola mounts .. when not using it, I put a (Motorola low profile) rain cap on it.
The factory luggage rack holes, I put to use by installing a luggage rack. The OEM dealer one is almost $900 in parts, a salvage yard one, compete was $150 plus a few bucks for the riv nuts (the factory riv-nuts actually have a sealant on the outside, and the bolts to be used do too)and a tool to install them properly.
I have the impression that nothing much was done after it came from the factory. I only found one spot where 3 wires were cut, in one harness that was spliced into the distribution box, near the brake pedal) Looks like they were for some sort of radio. I found that when hooking the speed sensor up to the GM Navigation Radio
We had just a little rain/snow around here, but I think I fixed it properly.
Ron