Hi,
It doesn't matter there's paint over it. You just make sure the paint doesn't make chemical reaction's you don't won't.
The shielding paint is used to make a 'cage of Faraday'. This is to get rid of interference. Like noise from TL-lighting, amateur radio stations and so on.
You just have to make sure that on some part the shielding paint has to connect to the earth wire, usually found on the back of the volume pot, or the wire that runs from the bridge.
I hope that answers your question.
Gerard