I just reported a bug on the Mint forum: https://forums.linuxmint.com/viewtopic.php?f=208&t=307676
But actually the bug is related to snapd. Each time my application gets updated, the shortcut at ~/.local/share/applications/*.desktop remains unchanged, therefore the Icons path soon become invalid. Therefore I need to manually replace all occurrences of e.g.:
how did these shortcurts get there ? by default snap packages install their desktop files into /var/lib/snapd/desktop/applications/ and the icons go to /var/lib/snapd/desktop/icons if you have anything snap related in ~/.local/share/applications you should find out what did put it there and make it not do that…
I believe this is the reason why I had to manually copy all .desktop files there:
Otherwise, if those files are not within /usr/share/applications or ~/.local/share/applications they won’t be listed within the launcher among other apps. Ok, At least now I remembered that I manually put it there as a workaround to the aforementioned bug with snapd.
I decided to apply a new workaround mentioned on the link above by using extended PATH and XDG_DATA_DIRS. Therefore, original .desktop files should always work as designed and apps will be listed in my launcher automatically. Hopefully the original bug will be resolved soon.