Yeah, I suppose that unlike Mario, where the enemies were explicitly the foot-soldiers of Bowser's army, in the original Zelda the enemies mostly resemble wild, untamed monsters who has just sprung up as a result of Ganon's evil spreading. It goes along with the series theme of Ganon being an archetype of pure evil whose presence corrupts the land itself.
Ganon becoming an actual human in Ganondorf changed this a bit; presumably he also had an army of footsoldiers in OoT, considering he was a prince(the Gerudos?), but they don't really come into contact with Link. With Wind Waker they needed enemies who actually have the manual dexterity to operate machinery and boats, because of the ocean. As you said, there are moblins, but moblins have always been a little too tough to just be the default mooks. Hence, Bokoblins.