A lot of the British boats got the steadily increasing armament treatment as the war progressed.
They mostly started off with .303 and .50 caliber guns, but by mid-war started sporting 20mm, 37mm, 40mm, and even the 6 Pdr. guns, as you mention.
A variety of single, double, and quad mounts, depending upon the vessel, period of the war, type – MGB or MTB and short or long hulls, etc.. It seems to have been a reaction, in my opinion, to the heavier armament of the S-Boats, and other German coastal craft, and the desire to be able to put more metal on their targets, when not attacking with torpedoes.
Apparently, during the very early to mid-war period, even machine guns and light cannon were hard to come by for the small, coastal forces vessels. By 1944 though, experiments/trials were progressing very quickly, and by D-Day, even some MGBs were getting torpedo tubes and being redesignated as MTBs.
Some boats needed deck reinforcing to carry the heavier weaponry.
Same goes for the S-Boats too, but they started out with at least 2 x 20mm cannons (fore and aft) from the start of the war, and by the mid-late war period, were sporting a single or double 20mm cannon amidships too.
Most retained the 20mm foredeck gun as a single mount, though there were plans for some boats with 30mms at all mounts (single, and double, IIRC). I think that only a few, if any of those were produced, due to the scarcity of the 30mms for the coastal forces vessels – most were allocated to their fighter aircraft, instead.
Rear mounts for the S-Boats were usually single 20mm, 37mm, or 40mm guns, though it appears from my analysis of late-war units, that at least one per flotilla of 8 – 12 boats would have a quad 20mm cannon aft, instead. Those were usually deployed in the rear-most position on ops, in case they were attacked by enemy fighter aircraft (presumably during the daytime, if late getting back from their night-time sorties).
Only one vessel, that I'm aware of, had their tubes mounted on the foredeck, and that was MTB-73 (or possibly 74?), for the St. Nazaire raid, as you mention. The torps were so fitted to fire over the anti-torpedo barrier(s), or locks.
I hope that helps.
You'll want to carefully balance the firepower and hull points for your scenarios for both sides, since numerous heavy guns can quickly make battles very one-sided.