Does every nail on a roof have to be sealed with Silicon?

I think you need to speak to the installer on this one

What kind of a roof is it? If it's shingle, no, the nails are under the overlapping shingle. If it is a metal roof, the nails or screws (preferably) should have had a washer attached before installing.

Check your local building codes. Call the inspector back. Did the inspector sign off on the job?

Like Sal85902 says. The shingles overlap the nails. As the shingles warm up they seal over the nails. They do not need to be siliconed. Any exposed nails do need to be siliconed but there shouldn't be any. Your inspector is mistaken.

Also contact the roofer. William and Sal are correct.

You did not say if this was a metal roof. I hope not because they get screwed on. If it was nailed in the valleys, you would eventually have problems.

Never heard of such a thing, usually on a shingle roof the nails are under the next layer of shingles. And a metal roof they use a nail head screw with a rubber gasket. Unless this some state contractor requirement, you could check with your State Contractor Licensing Board or your city planning department to see if this is a local requirement.

Talk to a different inspector or better yet, talk to the City/County head of the Building Dept.

I agree, this is suspect.

In my Specifications for Construction Documents, I have to specify nailing patterns to meet the Wind Shear requirements, per Code, but that’s not this.