I had a strange issue, with Firefox opening directories using k4dirstat, instead of dolphin in KDE (for example when you click the directory icon in the downloads list). The problem was quite obscure, and located in a very non obvious place: /usr/share/applications/mimeinfo.cache

I had to modify inode/directory entry there, to make it like this:

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inode/directory=kde4-dolphin.desktop;kde4-k4dirstat.desktop;kde4-kfmclient_dir.desktop;kde4-gwenview.desktop;

Before the change, kde4-k4dirstat.desktop entry was placed before dolphin, and that apparently made Firefox use it instead. Somehow doing it from KDE's System Settings > File Associations > inode > directory didn't affect that config file. Is it expected, or this file is not affected by the KDE settings?

That is unusual that you were forced to change the system wide file - as there is a local user copy of that file at ~/.local/share/applications/mimeinfo.cache which should be preferred. Can you check to see if that file exists and is writable?

If it does not exist, or is not readable / writeable then that would explain why the system wide version of the file was used.

It exists, and is readable/writable, but it doesn't have inode/directory entry in it. I added it to the local file, and reverted it in the global file - and it works good. But I see that local file is still disconnected from the KDE system settings MIME associations. Is it supposed to be updated when they are changed in the UI?

To the best of my knowledge, that file should be updated, yes.
As the 'mimeinfo.cache' file is a cache of data have you checked it's counterpart file ~/.local/share/applications/mimeapps.list?