If you don't mind, would you give some other examples for how this word could be translated? I tried the basic way of putting the kanji into Google Translate, and what came back spelled as "shadow" so my assumption was it might depend entirely on the context and is not per se meant as a descriptor for a person alone?
But I don't think 115 instances is negligible, either. vndb currently has the game sitting at around 30 hours playtime. How many repetitions of this single word would have to be in the og script to justify that? I'm not even saying the change of that to "incel" is the biggest problem. It sure as hell the most obvious one, but I can hardly imagine the srcipt didn't give them leeway to at least have half of these 115 instances replaced with something similar every so often? It's all around making this translation look terribly unprofessional.
Inkya comes from the japanese word for shadow that means shadow as in darkness/gloom, and kya is a shorthand for character. So basically it describes a person from the lower social circle in school. The opposite would be Youkya, the first part comes from the word for sun/sunglight and describes someone who'd be considered popular.
See, the thing is, both of those words describe people with social circles. Something a loner doesn't belong to, they're a separate category (bocchi) so I don't see it as a proper translation choice.
As far as an example for how to translate it, it gets tricky because they use that word as a nickname for the character so it has to be a word that can work as a nickname. A safe or neutral choice would be calling him Gloom, Gloomy or something like that but the translation already uses gloomy to describe him so they went with something more fitting for his other defining characteristic which is him being chick repellent. It also kinda barely sounds like Inkya, though I'd be speculating by saying they factored that in. So yeah, something related to being gloomy, drab would work. Maybe you could call him emo? He kinda looks like an emo.