Quite likely because the only dudes who knew Latin in the Middle Ages were in monasteries, and so they applied Latin words they learned to their circumstances. "Hey, it says here that when Romans brought in a new imported, inexperienced slave, they called them novicus. Let's use that for our newcomers! After all, we make them do chores, like slaves, LOLZ!"
https://www.etymonline.com/word/novice
Sure the root word might be Latin, (and so is a majority of European vocabulary), but the specific usage of "novice" meaning "newbie" in English, comes from the monastic orders, via French.
Monastic orders, which, in fact, did not "do stuff, like slaves, LOLZ", but were instrumental in preserving (or rediscovering) knowledge and technology from the imperial era.
This is the dictionary definition of shoshin from kotobank.jp:
> ② (「しょほっしん（初発心）」の略) 初めて悟りを求める心を起こすこと。仏道にはいったばかりのこと。また、その人。〔法華義疏（７Ｃ前）〕 ※正法眼蔵随聞記（1235‐38）一「或は初心未入(みにふ)の人意得(こころう)
> Because practice within realization occurs at the moment of practice, the practice of beginner's mind is itself the entire original realization.