As far as my experience with an EC060 goes there's no noticeable difference in speed against a full featured 040.
I bought an '060 from a UK Amiga hardware dealer a while back (no clues given, other than the name contains the word ANAL) which instead of the fully loaded '060 I ordered turned out to be equipped with a 66Mhz EC version. As a result, all my FPU/MMU preferred programs fell over, and the only thing that did work was Frontier. This was played at an identical framerate to my 40Mhz 040 - but in fairness, this is probably due to the lack of 060 specific support in a game coded way back in 1993, long before the 68060 actually appeared.
Moral of the story - MHz isn't everything!
