I don't think he's a joke character, I think that Hussie liked Equius more than you're implying. He gave Equius themes that he enjoys a bunch in his writing, you can tell because they come back in Dirk too. Also ARquius was awesome.
I'm a big Equius fan, and I understand yeah he's got the classism of Alternia ingrained into his stunted socialization which is awful as a person but great as a character/literary device. We had to see what the hierarchy most of the world runs on is actually like to flesh out Alternia.
He's so essential to so many cool parts of the troll session but in a creepy background way. I still don't think he's a joke character but his role in the story is just inherently funny. Yeah you can get whatever robots or robot parts you need, he will clearly just make stuff for you with seemingly no compensation, but you have to deal with the awkward sweaty horse freak. It's great. Even Equius haters have to admit the story is better for having him in it.