Hi,
Yes, limescale is a calcium or magnesium carbonate which is dissolved by any acid. Vinegar is a weak organic acid, otherwise known as acetic acid. If vinegar or the dissolved product gets into the water the effect would be to lower the pH which is not really a big deal. Otherwise, in small amounts there should not be any toxicity. If you wanted to play it safe you could just do a water change afterwards. Organic acids are constantly being produced in the aquarium so this one is not a big problem. I'd prefer to use vinegar than to use some of those commercial limescale removers.
Cheers,