It's the +skills that provides the difference in damage on that display screen. However, that display screen is often inaccurate. It's called the Lying Character Screen (LCS) for many reasons.
If you consider the -resistance on Griffon's that isn't on Shako (and isn't dislayed in the LCS), then Griffon's is almost always far superior.
For example, (let's use some simple numbers):
20k average damage with Shako
19k average damage with Griffons (-25% resistances)
Monster with 0% resistance:
20k with Shako
(19k * 1.25) = 23.75k with Griffons
Monster with 50% resistance:
10k with Shako
(19k * 0.75) = 14.25k with Griffons
Monster with 90% resistance:
2k with Shako
(19k * 0.35) = 6.65k with Griffons
The only time Shako is better than griffons is when you've got a monsters resistance lowered to the max without the Griffons (Infinity merc + Cresent Moon sword + 0% base-resistance monster) - but those times don't matter because the monster will die very fast no matter which helm you choose. - it's the monsters that have a high resistance where the Griffon's will really shine (and, you have to admit, it's the highly resistant monsters that're going to slow you down anyways).