I've got some experience acid-cleaning hardness mineral scale from various metals. I work at an industrial wastewater treatment facility that receives and treats process wastes from a number of different chemical manufacturing companies. We use lime (Calcium Hydroxide) to neutralize the mostly acidic wastes we receive from the buildings, but from time to time we have to mix up dilute acid solutions and circulate them through piping and valves to clean the calcium scale that forms from years of (ab)use.
Muriatic acid is another name for hydrochloric acid, and it is not very friendly to metals. It will attack iron, steel, bronze, aluminum, copper, and a host of other metals more or less uniformly, but it is particularly bad for stainless steel. I wouldn't use it for any cleaning unless you had no other choice *and* you used a very weak solution (pH above 2.5) *and* you limited the exposure time to just a few hours.
Vinegar (acetic acid) is a bit more benign to most metals you'd find on a boat, but it does still attack them. It also smells terrible, and because it's a weak acid it's also not very effective at cleaning scale. It works, but it takes a long time.
The best acid we've found at work that cleans up just about anything (including calcium carbonate, which is literally hard as a rock and very difficult to remove) is Citric acid. Now, I'm not talking about orange juice here! But at a concentration of about 5% by volume, citric acid positively EATS through mineral scale while leaving the metal beneath mostly unscathed.
Granted, just about any acid will corrode iron and steel, but at low concentrations Citric Acid is far more forgiving than any of the mineral acids. It also works far better than acetic acid! But the best part is that it is relatively safe for stainless steel, and it's less damaging to aluminum, brass, bronze, and copper than any of the mineral acids. It is also safe for most rubbers, plastics, and fiberglass.
Only real downside is that it's a lot more expensive than muriatic acid, but if you buy it in bulk powder form you can still get it pretty cheap.
Just my $.02...
Adam