It does look like scab to me. With those seedlings as small as they are, and the scab as bad as it already looks, I doubt that these will do well regardless of what you do.... I hate that!
Best thing that you can do about scan is begin with types pecans that are known to be scab free (resistant) in your area.
I'm not sure of Italy, but here in the southern states, Dooley, Hirschi, and Maramec are so prone to scab, that they are just avoided here.
Jenkins and Syrup Mill (maybe Syrup Hill?) are good all around cultivars because they have excellent scab resistance (for now...fungal disease is ever evolving) and they also have excellent self pollination rates. (Pecan trees usually produce pollen and buds at different times to increase genetic diversity but these 2 cultivars have pollen and bud times that overlap, very nicely, per individual tree. This means you can plant just one of this type and still get excellent production! )
USDA Zone 7b/ Sunset Zone 31