At risk of being called a wokie or whatever, it’s because being a female character, dark skinned, and having a “black hairstyle” all at the same time makes them not conventionally attractive to white/Asian people. Lenora is probably the only exception as both a dark skinned black female Pokémon with an Afro who gets a fair amount of fanatics. Even still, she probably the most conventional, familiar looking ‘unambiguously’ black woman character archetype you can come up with. She’s a strong independent African American woman with motherly vibes, who’s middle aged, kind of fat but not really, dark skinned but not to the point of being night dark, and has curly hair. Big whoop.
Meanwhile, Agate is VERY extremely dark skinned, with a more African look in regards to hair and clothing, while Amarys is also fairly dark and has weird fantasy Bantu knots. Not to mention they don’t fit tried and true stereotypical character archetypes for unambiguously black female characters (like how Amarys is stiff and taciturn). They’re too daring and stray too far from Asian/European beauty standards, so the majority white/Japanese Pokémon fanbase isn’t in to them like that. A dark skinned female character design either had to be fantastic or at least inoffensive to compete with even the WORSE of pale skin female character designs, like Penny.