I thought / have observed that the spelling "chili" (single letter l) was used for the US / Mexican dish called "chili con carne", and the spelling "chilly/chillies" was used for the hot pepper that came from the Americas and spread to much of the world.
Edit: Wikipedia says both spellings are used for the hot pepper:
https://en.m.wikipedia.org/wiki/Chili_pepper
Edit 2: See the Spelling and usage section.
It does not mention the y ending, but I have seen it in India.