Two separate policies in my name with 2 different named drivers and one of them had an accident, do I lose NCB on both?

Only the NCD on the car onto which your son is insured will be affected. You will still retain the full no claims on the policy where there's just you and your wife.

On the car which had the accident, you will lose NCD because your son is just a named driver and only policyholders are entitled to NCB. Therefore any claims made by the additional drivers (your wife & son) on the policy will result in you, the policyholder, to take the responsibility. So depending on how many years no claims discount you've got (and whether it's protected or not), your NCD might be stepped down (by 2 or more years) or wiped off completely.

Your other set of NCD remains safe as you're not going to put up a claim to that insurer and on renewal, there won't be any problems because the accident/claim will be recorded against your son's name.