Hi Michal,sorry for the very long silence on this report. The problem is still there in nemo 6.6.4-1 in unstable: a symlink on the desktop to /usr/share/applications/org.gnome.Calculator.desktop is shown with its file name and a generic icon, and double-clicking it opens the "Untrusted application launcher" dialog.
The upstream issue [1] was closed in 2020 without a fix (the suggested workaround was to make the system file executable as root), which is why bts-link added the fixed-upstream tag; I have removed it.
The cause: nemo trusts a launcher if it is executable or if it lives in a system data directory, but for a symlink the directory checked is the one of the link, while the permissions read are the ones of the target (root-owned, not executable). I have proposed upstream [2] to resolve the symlink and apply the system directory check to the file it points to, so a link to a system launcher is trusted and one to a file elsewhere is not. It is tested in a VM with nemo 6.6.4 rebuilt with that change.
Until then, the "Launch Anyway" button of the dialog starts the application, and copying the launcher to the desktop instead of linking it (then making the copy executable) avoids the dialog altogether.
[1] https://github.com/linuxmint/nemo/issues/1130 [2] https://github.com/linuxmint/nemo/pull/3846 Regards, Fabio
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