I read the excellent 'Motor Gunboat 658' late last year.
At least in the Mediterranean the British seemed to think that their were superior to their German opponents in every capability except for outright speed. This feeling was doubly reinforced when they started operating with US Partol Boats fitted out with better radar (funnily enough, it was British designed), who allowed them to pick up targets well beyond visual range and manoeuver for the kill earlier. The biggest danger to MTBs, MGBs and 'Dog Boats' seems to have been mines rather than enemy surface action.
The MGBs had 1 6 pounder, a twin 20mm, two twin .50s (later replaced by two single 20mms, and then two twin 20mms), a 40mm pom-pom (later replaced by another 6 pounder) and a couple of twin Vickers .303 mounts. With 4 1000 hp Allisons in the back driving 4 screws, they were no slouch in terms of speed either.
MGB 658 was credited with the sinking of 1 Escort Corvette, 3 E-boats as well as 9 other ships. It was also credited, remarkably, with 3 Fw-190s (2 in one action) 2 Ju-88s and a Do-217. 1 of the Fw-190s, the Do-217 and 1 of the Ju-88s were all destroyed on lone long-range patrols by the crew, so the boats certainly weren't defenseless against fighter and bomber attacks.