I was told by a vet tech (before I found a proper pig vet), who was, at that time, looking in the Big Book of Pestilence (which probably had a boring science book name) that guinea pigs --always-- have mites, but unless they are ill or injured or dirty, the mites are dormant, or there are only one or two living ones, hence the occasional scratch.
This is how it was explained to me, translated from the Big Book of Pestilence: Think of it like brine shrimp--the naturally occuring ones, not sea monkeys--that live in puddles, and they eat and live and lay eggs. If the puddle dries up, then the eggs lay dormant until something, like a rainstorm, wets the egg and it hatches as if nothing ever happened. They're just waiting for a foothold.