Harlequin paint jobs were all custom orders so it would be difficult to figure how many were done that way.
I would say very few Yo Eddy's have the harlequin paint job as it was losing popularity towards the end of the Somerville era and it was very expensive
The sunset fade and the two-color grello and blue were the most popular customs on Yo Eddy's as far as I can remember but I have no idea how many were produced since that was not my area.
Mike Flanigan might have a better idea on numbers but I know he does not contribute here.
If you've got a harlequin Yo, hold on to it since it would be very collectible now.