I think the Alliance isn't so much buying its munitions (like proton torpedoes) from legitimate suppliers as they are hijacking Imperial (or corporate) shipments. Sure, they have some limited manufacturing capabilities, but I doubt it's enough to keep up with demand. Shortages of pretty much everything is SOP for any guerilla force, so justifying why a ship doesn't have torpedoes for its launchers isn't much of a stretch.
And if you're comparing the Y-wing to contemporary fighter jets I think it's more like an F-111 or an A-6; a heavy, ungainly fighter-bomber that can put a lot of boom on a target but needs help to keep faster, more manoeuvrable opponents off their backs while they deliver the payload.