In fairness, for search, allowing multiple ways of typing the same thing is probably the best choice: you can prioritise true matches, where the user has typed the correct form of the letter, but also allow for more visual based matches. (Correcting common typos is also very convenient even for native speakers of a language — and of course a phonetic search that actually produced good results would be wonderful, albeit I suspect practically very difficult given just how many ways of writing a given pronunciation there might be!)
As a counterexample, conflating two different glyphs as if they were the same can lead to the inability to search for a particular term. E.g. in Spanish these two words (cono, coño) have very different meanings. If I'm searching for one I don't want to see results pertaining to the other one. It would be like searching for "sheet" and getting results for "shit".
It depends on how the search is implemented exactly and what the context is, but assuming I've searched for "cono", I would expect results that directly match "cono" to come first, then results that also match "coño".
Similarly to how I'd expect to still get reasonable results if I type "beleive" instead of "believe".
That said, this is obviously pretty context-dependent, in some settings it will make more sense to do an exact-match search, in which case you'd want to differentiate n and ñ (while still handling different possible unicode variants of ñ if those exist).