There's been plenty of discussion about how weird this is in a series full of racial representation problems (Nagini is an Asian woman who has heretofore been portrayed literally as an animal), but there hasn't been as much discussion about how weird this is in terms of character and plot. Humans who can turn into animals are, of course, nothing new in Potterland, but this revelation raises a lot of questions about Nagini, chiefly her relationship with Voldemort, that are frankly better left unasked.
In the main series, Nagini is Voldemort's most treasured companion, the creature to whom he shows by far the most affection and loyalty. His belief that she will always be by his side and that he can always protect her is so great that he makes her one of his horcruxes, embedding a piece of his dang soul in her. It always seemed like an interesting -- and most importantly, intentional -- element of his character. He is so disconnected from humanity that the only creature for whom he can show anything close to love is an animal. His ignorance of the power of human love is the fatal flaw that ultimately brings him down.
So what the hell is going on here? Did Voldemort know she was a human? It's not like he could just pick up an evil snake at PetSmart, so it seems more likely that however they were brought together, he must have known her history. How on Earth did they meet, anyway? It's not clear at what point Nagini transformed permanently, but given that The Crimes Of Grindelwald takes place the year after Voldemort was born and Nagini isn't that old, it's nowhere near impossible that he met her when she was still a sexy snake woman.