The OED3 (2004) has the football slang noun from 1968 and the verb from 1975. It doesn’t give an etymology for this particular sense.
Nutmegs, in addition to the plain nuts, is also slang for testicles going back to the 1680s, according to Green’s. The OED marks it as obsolete, with a last citation from 1846. Green’s, however, includes two later citations, one from the journal Maledicta in 1980, which may be a reference to the older usage. The second is this:
1999 [UK] Roger’s Profanisaurus 3 in Viz 98 Oct. 21: nutmegs n. Balls that hang between a footballer’s legs.
This last citation clearly associates the two senses. But if the slang sense of testicles was really obsolete, that would make that origin less likely. It still could have been recoined/revived in the twentieth century by footballers, though, especially given the existence of nuts for testicles.
I’m skeptical of the Cockney rhyming slang explanation. Rhyming slang is often used inventively to create an explanation, and it seems unlikely that nutmegs = legs would have caught on with an already existing slang sense meaning testicles. And I know of no evidence to suggest that nutmeg ever meant to pull something over on someone. So that third one seems to have been invented out of whole cloth. I don’t doubt that nutmegs, which were once quite rare and valuable, were the subject of all sorts of con games, but I don’t see any reason to think such scams spawned a slang term.