While there is no official game for the Nintendo 3DS, the "CIA" files you see mentioned online refer to unofficial fan ports or prototype versions. The original 3DS port promised during the game's 2014 Kickstarter was officially cancelled and replaced by the Nintendo Switch release in 2019. The Status of OMORI on 3DS Official Cancellation
However, due to the magic of homebrew, there are people claim to run OMORI on a 3DS: omori 3ds cia hot