Ubuntu 18.04: "Add to Favorites" missing for certain qt-based applications?
A convenient workaround for me was adding it to my favorites from the omnibar.
It is completely weird, unpredictable and unexpected UX.
I confirm your results on Ubuntu session (GNOME Shell) in Ubuntu 18.04 LTS and even with 19.10 (development version).
My first thought was that Exec field pointed to some symbolic link, but all files declared in it are simple ELF executables.
What is also bad that these desktop-files do not have OnlyShowIn directives...
I do not have this issue on Unity, MATE (using Mutiny panel layout) and Lubuntu sessions in 18.04 LTS and even with 19.10 (development version).
Also I'm able to dock these applications into Cairo-Dock, Docky and Plank.
So it is a bug in GNOME Shell.
I reported it as bug 1840474 to LaunchPad (really it is a duplicate of bug 1768609 from 2018-05-02).