I suppose it would likely depend on the era of the map for me. Especially in the case of Charybdis, I think the symbol would likely appear to warn of that area's particular frequency of whirlpools. Given the speeds of sailing vessels and danger of running aground back then, it could be considered a danger enough to mark with a whirl pool. Modern maps would more likely have some sort of line indicating a hazard area with the label "WHIRLPOOL ZONE" or some such. With more ancient maps, it may well have been penned by a culture - or just even just the explorer - who mistakenly thought the whirl pools were common because they saw 3 of them in the 4 days they were in the area.

And in looking on Wikipedia, I found this 16th Century map depicting the Moskstraumen (Maelstrom) in Norway. It shows a ship caught in a whirlpool.