Can Vent Flashing Nails Be Exposed On The Roof?
They probably should be dabbed with roofing cement, but they tend to self-seal to some extent. It's unlikely that they'd leak significantly. 

Also concerning is the fact that raw steel nails were used. They'll rust and stain the roof over time. Cement will mostly remedy that as well.

FYI, I don't consider those nails necessary anywhere short of a hurricane zone. Hidden nails and the sealing strips on the shingles hold it all down just fine.