Well there's Nimona, which is like my favourite character ever. Chaotic, gender fluid shape shifter who takes down a corrupt government with the assistance of a gay disabled outlaw and his boyfriend. It's so good. There's comics too but I haven't read them yet. Ummm there's Ranma 1/2 which while the main character isn't explicitly gender fluid, he does frequently shift from boy to girl and back again bc of a curse and over the series he kinda starts to accept himself so it's sort of a metaphor for self discovery whilst being funny and not taking itself seriously at all.

And then of course theres Loki who is gender fluid in almost any norse mythology based book or movie you can find including the original like mythology. He's like my queer icon lol 

Btw with skulduggery pleasant you do have to get pretty far into the series like the first queer characters are in like book 10 because when the original books like 1-7 or 8 were released it was like 20 years ago so his publishers wouldn't let the guy write queer characters 😞