Yep, pretty much. This series seems to have a problem with female characters, and not just monsters. I also noticed that whilst the male characters fight with swords, pickaxes and axes etc, the female characters only fight with bows and arrows. Also, there are a LOT more relevant male characters in the series compared to female...
For male characters we have Gameknight, Herobrine, Erebus, Malacoda, Xa-Tul, Feyd, Reaper and as you mentioned Charybdis (who is in fact named after a Greek deity of water, who was female), Entity303, Monkeypants, Crafter, Herder and Digger. That's 13 relevant male characters. Not counting Weaver, Fencer, Carver and Smithy. That's 17 if they count.
As for female characters we have Monet, Hunter, Stitcher, The Oracle, Shaikulud and Shaivalak. That's six. You could also include Ba-Jin and Baker (from arc five), if they count, but even then, it's still less than half the amount of the male characters.
Baker is the only female character (NPC) I mentioned who fights with a sword rather than a bow and arrow. Even background female characters always fight with bows and arrows.
In every book, there is a character who dies for Gameknight, and if I recall, there is only one woman, Tiller, not counting Fletcher, who appears for like one chapter.
There's just such a great gender imbalance in this series.
(Also The Farlands, I don't know if anybody else here has read them, are a bit iffy too. Again, there are a lot more relevant male characters, and the only female villain is a spider, again. There's a scene where the characters see what's inside them, and the male characters are all portayed as strong and confident, whilst the female character is portrayed as weaker and softer and needing protecting. Another female character, Fencer, is just so off too, she's basically a stalker and keeps intruding on the main character's boundaries and receives no punishment and feels like a stereotype you'd find in old, somewhat sexist, films. The female character, Planter, fights with a sword in the first book, but then she took switches to using a bow and arrow too.)
So yeah, overall both GK999 and it's spinoff feel a bit off in gender balance for me, as much as I love them.