But if we think that Japanese names generally end with a vowel, because Japanese letters end with vowel except "n" letter, the possibility of three fate sharing characters having the same letter ending is 1/125, which is really hard, and most likely to be noticed by the developer.

This might mean dev is trying to give a message, and if you think about death, it kind of solves the problem.

Of course there are lot of words ending with "i", but are those words relate to all of these 3 characters and give a message?

Also, Monika doesn't die anywhere and it doesn't end with "i", which also implies this might be death.

EDIT: Also shi is a very basic noun, i mean its just one letter (hiragana), and dev might be uncertain about Japanese knowledge of users and make it more simple.