@carmenfdezb, actually, looks like I found it by accident. new flatpak has environment generators and those confused SFOS. For example, while starting ssh session, I was getting

NOTICE: Env value ignored: XDG_DATA_DIRS=/var/lib/flatpak/exports/share:/usr/local/share/:/usr/share/

That also resulted in inability to scp to device. All turned out to be caused by env generators. As soon as those were removed from device, icons disappeared as well.

New flatpak has been just compiled. Update to that, reboot device, and it should all be fine.