Why 'clever clogs' as a humorous description of someone who gives a bright answer? Is it just that the repeated 'cl' suits the phrase or is there some significance in the choice of 'clogs' ?
Given that cleverboots has also been used, I imagine your idea re alliteration of 'cl' is the correct explanation. On the other hand, I'm not too sure why brightness should be associated with footwear!
Not only pants, J! Sides, jacks, kins guts and pots have all also been tacked onto clever to describe a 'bright' person...and I won't even mention the diminutive of Richard in that role!