This happenned to me, I was given a ban for 56 days and, what the magistrate at the time referred to, as a "nominal" 6 points. When I got my licence back the offence was there but with 0 points so clearly "nominal" meant that it was a 6 point offence but banning meant they didn't count for future totting up, though the endorsement is on the licence for the usual amount of time. So to answer your question he will have 3 points when he get's his licence back. There's no such thing as an "automatic" ban, the JP always has discretion but a ban is almost certain in this case.