In your retroarch/assets/xmb/*
directory you can find several icons for systems and content:
example:
xmb/systematic/png/
'Sega - Mega Drive - Genesis-content (E).png'
'Sega - Mega Drive - Genesis-content (J).png'
'Sega - Mega Drive - Genesis-content.png'
'Sega - Mega Drive - Genesis-content (U).png'
'Sega - Mega Drive - Genesis HAA-2502 (J).png'
'Sega - Mega Drive - Genesis HAA-2510 (J).png'
'Sega - Mega Drive - Genesis HMJ-0300 (J).png'
'Sega - Mega Drive - Genesis MK-1461 (U).png'
'Sega - Mega Drive - Genesis MK-1601 (E).png'
'Sega - Mega Drive - Genesis MK-1631 (E).png'
'Sega - Mega Drive - Genesis MK-1631 (U).png'
'Sega - Mega Drive - Genesis MK-6100 (U).png'
'Sega - Mega Drive - Genesis.png'
You can change the name of your playlist to one of the names and RetroArch will use the right icons. (could be a problem on Windows 'cause of the () brackets)
e.g. Sega - Mega Drive - Genesis MK-1461 (U).lpl
Remember to change the entries inside the playlist as well
"db_name": "Sega - Mega Drive - Genesis MK-1461 (U).lpl"
You can also put your roms in a Sega - Mega Drive - Genesis MK-1461 (U)
directory and do the scanning process once more
[EDIT] I think you have to rename the icons, otherwise it will use only the system icon, but not those for the content.
For example rename
Sega - Mega Drive - Genesis MK-1631 (U).png
Sega - Mega Drive - Genesis-content (U).png
to
Sega - Mega Drive - Genesis (U).png
Sega - Mega Drive - Genesis (U)-content.png