Why are some iTunes Store songs marked as CLEAN when no EXPLICIT version exists?
I just had a look at differently tagged files.

The responsible ID3-tag is rtng (short for rating). If set to 1 the song will be marked as EXPLICIT, while 2 shows up as CLEAN. Every other value leads to no label.

I recommend Kid3 as a tag editor.

EDIT:
According to this and this, the values should be 2 (CLEAN) and 4 (EXPLICIT). I can't reproduce those, maybe someone copied it wrong...