One of the things I absolutely hate are “Face Nails”.

Face Nails are exposed nails.

In the context of roofing, a Face Nail is any nail that isn’t covered by roofing material. You can absolutely have covered nails that are still a leak vector, but that is a different topic.

A Face Nail is a Face Nail, and nothing can change it.

A well installed shingle roof with good quality shingles has a lifespan of roughly 20 years, more or less.

Sealant of ANY kind that is exposed to the elements will NOT last 20 years. Or even 10 years. MAYBE FIVE.

Covering nails with sealant is a very, very short term sealing method. I don’t care WHERE on the roof that exposed nail is, covering with Sealant as a solution is a piss poor decision, representative of low quality.

Nails or screws in flashing, regardless of covered with Sealant or not, is the exact same issue. Piss poor quality.

A lot of pipe boots will have nails at the bottom of the pipe flashing piece, and then the nails covered with sealant.

The metal fascia along the edge of your roof is frequently nailed in place – many roofers will also address fascia issues – and again, exposed nails are a vector for water infiltration.

Your roofing contract should state that their will not be any face nails, regardless of covered with sealant or not, regardless of where on the roofing project the nails are installed. This means shingles, flashing, counterflashing, fascia, and any other parts of the construction on the roof.

You owe it to yourself.