I'm happy to announce that I have discovered the source of my problem.
So, I checked the key map file (/opt/retropie/emulators/vice/lib/vice/C64/sdl_sym.vkm) and I had found in its last line this:
0 -3 1
which is the 'second RESTORE key' responding to the scan code 0. I don't know what does the 'second restore' mean, and I'm not sure what the 0 scan code stands for. I guess it somehow connected with the 'do nothing' action in the joy-map file (which is also 0 coincidentally).
Commented out this line and now I can shoot clouds with Loco, I can fire happily with WoW (which definitely stands for Wizard of Wor and not that new stuff), and... and I'm a happy man!
Thanks for reading!