When overriding a .desktop file which exists in /usr/share/applications by placing a desktop file in .local/share/applications with the same name, both applications are found and shown by wofi in drun mode. I could not find an option to change this behavior.
It would be good if only the .desktop file in .local/share/applications would be shown in this case (this is the same behavior rofi uses), perhaps this can be an option.
This is actually the behavior though? At least on the current tip only the desktop file in
~/.local/share/applicationsshows for me, could you please clarify the version you're on?