Are the irregular demonyms limited to places where Southern Germanic dialects/languages are spoken, or is it just coincidence that your examples are all in Switzerland/Austria?
Recall also that residents of München are not Münchener but Münchner.
Recall also that residents of München are not Münchener but Münchner.
Up until the late 1700s, the trailing "-e" in words like "Füße", "mache" and so on were intentionally dropped in most of (Catholic) Southern Germany because it was associated with Luther's translation of the Bible and therefore considered heretical.
The effects of this are still present in German (e.g. the German word for "door" nowadays is "Tür" but "Türe" is still an archaic or rare variant you might encounter, likewise you might colloquially see phrases like "ich seh'" instead of "ich sehe"). If the places with demonyms that drop the "-e-" in places ending in "-en" are mostly in South Germany, that might explain why they differ.
Note, however, that the official pronunciation of "München" according to the German wikipedia actually drops the "-e-"[1] (rendering it in IPA as [ˈmʏnçn̩]), so "Münchner" is actually not as irregular as "Zürcher" (where the local pronunciation of "Zürich" actually drops the "-ch", not the "-i-"[2]).
[0]: https://de.wikipedia.org/wiki/Lutherisches_e (German)
[1]: https://de.wikipedia.org/wiki/M%C3%BCnchen (German)
[2]: https://de.wikipedia.org/wiki/Z%C3%BCrich (German)
Hannover - Hannoveraner
Bremen - Bremer (regular might be Bremener like Essen - Essener)
Jena: People who live there are "Jenaer", people who are born there are "Jenenser".