ok, i found a workaround

i saw that chromium uses xdg-open and xdg seems to take care about the
MimeType values in .desktop files

so i created a new desktop file for Lotus named
/usr/share/applications/LotusNotes8.5-url.desktop with this content

[Desktop Entry]
Encoding=UTF-8
Name=Lotus Notes 8.5 Url
Type=Application
Exec=/opt/ibm/lotus/notes/framework/../notes-wrapper %u
Icon=/opt/ibm/lotus/notes/framework/shared/eclipse/features/com.ibm.notes.links.feature_8.5.2.20100811-1131/icons/notes.ico
Terminal=false
Categories=Application;Office;
MimeType=x-scheme-handler/notes
NoDisplay=true

note the %u instead of %F and the NoDisplay key

same thing for Spotify with /usr/share/application/spotify-uri.desktop

[Desktop Entry]
Name=Spotify
GenericName=Spotify
Comment=Listen to music using Spotify
Icon=spotify-linux-512x512
TryExec=spotify
Exec=spotify -uri %u
Terminal=false
Type=Application
Categories=Qt;AudioVideo
MimeType=x-scheme-handler/spotify
NoDisplay=true

i don't know if this is the right way to enable custom url-handlers
so, Are the gconf values deprecated?

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https://bugs.launchpad.net/bugs/788673

Title:
  unable to open link with custom url-handlers

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