The main reason I stopped using programming ligatures that much is that many languages actually support Unicode characters in the source code, and this is actively used in some projects I work on.
It then becomes important to see the difference between ASCII approximations and real Unicode symbols, since this is relevant e.g. when searching for a symbol in your code base or to see at a glance whether usage of Unicode vs. ASCII etc. is consistent.
The only spot I still kinda use such a feature (prettify-symbols-mode specifically) is in LaTeX, where Unicode math is more rare and long equations become nearly unreadable without some kind of rendering in the source code.
It then becomes important to see the difference between ASCII approximations and real Unicode symbols, since this is relevant e.g. when searching for a symbol in your code base or to see at a glance whether usage of Unicode vs. ASCII etc. is consistent.
The only spot I still kinda use such a feature (prettify-symbols-mode specifically) is in LaTeX, where Unicode math is more rare and long equations become nearly unreadable without some kind of rendering in the source code.