Until the 20th century phrase had exclusively the meaning I always thought it had, and that meaning dates back to the 1500s (spade = gardening tool).

In the 1920s some people started using "spade" to mean "person with dark-toned skin" (because spades are black in a deck of cards, so spade the gardnening tool => spade the suit in a deck of cards => poc). I've never heard "spade" used like that before, and the article suggests that use of "spade" remains fairly esoteric, but it's apparently in wide enough use that dictionaries have picked up on this meaning.

The article doesn't ever establish that the phrase itself is used as a double entendre. In a quick saerch, I can't find any in-the-wild uses of "Call a spade a spade" that evoke the double meaning.

TBH I think the article's advice is sound but also extremely jaded ("Rather than taking the chance of unintentionally offending someone or of being misunderstood, it is best to relinquish the old innocuous proverbial expression all together"). I'll stop using the phrase, but doing so feels like assuming the worst of my interlocutors' intelligence and intent.