The problem of E.K. has been "resolved" many times. Edward Kirke, who attended Cambridge at the same time as Spenser, and was also a friend of Gabriel Harvey, was for many years regarded as the obvious choice (De Selincourt xiv.), but it could have been no safer to sign one's own initials to the sometimes heavily polemical glosses than to the eclogues. In recent years the preferred assumption has been that Spenser himself is E.K. (Sommer 8), and this is supported by many internal and external evidences. ... Yet this is not proof that Spenser is E.K.; it is at best evidence that Spenser was on the committee that created and sustained him. Arguments have been advanced for every member of the Areopagus, including Sidney, Harvey, and more recently Fulke Greville (McLane 280-95). In the end, we are left with no more of E.K. than the Areopagites have given us, and they protected his identity for the remainder of their lives. What we have of him, however, can afford to stand on its own. His contribution is a highly interesting text that forms an integral part of The Shepheardes Calender, amplifying the gist of the eclogues as needed, fine tuning our sense of the poet's technical attainment, erudition, and allegorical intent, yet at the same time deliberately adding confusion where it is needed, in order to distract powerful and potentially vindictive readers.That is from this informative online edition of the poem.
Now, for a while I was leaning in the direction of the argument that 'E.K.' is actually a formal embodiment of the generic identity of the poetry, and was simply enough short for 'Eklog(ue)'. But now I'm wondering about Fulke Greville. Reverse his first name and we have: E.K. Luf.
And indeed, this need not be exclusionary. Because what is the English 'F' if not a crossbarred gamma? And did not Greville sometimes spell his name with an 'O' rather than a 'U'? And what is EKLOΓ if not a variant of the word 'Eclogue'? I rest my case.