The problem is solved, but I'm not sure to understand.

After posting my answer, I did the following:
- as /home/user/.config/meegotouchhome-nokia/launcherbuttons.data gets corrupted on startup, I removed the permissions on the file (chmod u-rw), and I rebooted.
- after reboot, my launcher screen was completely changed, the order of the applications was not the same as before, and the quick launch icons were not there. But something was solved: after I reflashed the device a couple of days ago, I got some of the basic icons twice. Some of them disappeared finally to be displayed only once (like message), but some others remained twice (like maps). And this has been fixed.
- then i reset the rights (chmod u+rw) and I rebooted,

and now everthing seems fine. Quicklaunch icons are back (BTW, these are the ones I selected with Shortcuts without success), and I've only one icon for each basic app.

No idea why removing read rights on the .data file finally fixes the issue, but at least now it's ok.