At some point, the original author decided Monokai was a good name for both the website and the colorscheme: https://monokai.pro/
A different author ported the theme to Vim, and named this version Molokai to avoid confusion with the original author: https://github.com/tomasr/molokai
That's likely to be pretty frustrating to people for whom N and L are the same sound.
The loss of the distinction in Cantonese is fairly recent; Chinese terms borrowed from English via Cantonese all obey the distinction, using characters that indicate the correct consonant when read in other varieties of Chinese, and you can find old English-Cantonese dictionaries that talk about how certain Cantonese accents don't make the distinction (implying that "correct" Cantonese of the time still does, which is not the case today).
And in this case, Molokai isn't the name of a place, it's been chosen solely for its phonetic similarity to "Monokai".
If I found a new Harverd University, I may be able to justify that, but I certainly can't do so on the stated grounds of "in order to avoid confusion".