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Don't know anything about Zenmap specifically, but:

All the non-flatpak links in Linux (not only Gnome) are actually .desktop files, and they live either in /usr/share/applications/ for system-wide installed applications or in ~/.local/share/applications/ for user applications. I haven't traced where flatpak .desktops live.

.desktop is a text file, easy to read. You need Exec= line, that's the actual command that gets executed.