Would there be any electrical issues if a grounding point had a bolt welded and powder-coated or is it better to drill a hole, weld a nut to the frame and then powder-coated?
If there is no metal to metal contact, there is no ground. That applies to both of your scenarios. The powder-coating will act as an insulator. Personally, I would drill the hole in the frame, install a bolt through the hole. Powder-coat that so that there is a bare spot under the head of the bolt that doesn't get covered. Then use that bolt to install your ground so it is pretty.
You could run a tap through the bolt after powder coating
You could add a step to your process.
After everything is complete.
Nut welded to frame
Complete Powder coating
Run a tap through the nut to clear out any powder coating in the threads so you have good metal to metal contact with your grounding bolt. The tap should not have any negative effect on the nut, it should just clear out any powder coating that got powder coating sprayed into the threads and baked in.
That way, you will have good metal to metal contact for your new ground.
Image of a tap