Working on a mock inspection today I found that all of the flashing boots (plumbing stack, Service mast, furnace and WH thimbles) had exposed nails which are rusted. The endcaps of the ridge also had exposed nails which had begun to rust also.
Should these be called out as in need of repair (sealant or replacement)?
Roof is about 10 years old- showing signs of age- but nothing major.
IMO…i’d recommend sealing…nothing more
Nail heads should not be exposed on any portion of the roof or flashings.
I recommend dabbing roofing tar on top of all nail heads.
My opinion is that yes they should be pointed out. Unfortunately items such as the boots you describe do at times and dependant upon product and placement, require through fastening, no way around it. In the event of ‘through fastening’ the head of the fastener must be sealed, another means of properly through fastening is to use a washered fastener such as would be used for installation of metal roofing.
Another point to be made, the majority of the boots that are available are junk. I have tried various brands, I favor the Oatey with metal flange and rubber seal, however I have found that the sun’s UV rays eats them all up. Look closely at the rubber seal (for those who do get up and walk the roof…not wanting to start a debate on that issue) often they will develope cracks or splits that will allow water to get in however you may not notice it in the house due to the way a vent pipe is buried inside a wall.
The addition of sealant on the top of the nail heads would be reasonable for an improvement if the boot is in satisfactory condition. Replacement of the boot would not be needed if there is no leakage.
PS, I have been working outside in the 20+ degree weather we are enjoying in PA, I would love to come to TX and change these out for you…I usually get $150 each plus airfare and expenses.
Since it is only -8 to +20 over here I will come an fix yours for $155 each plus airfare and expenses. ha. ha.
Marcel 
“Numerous exposed nail heads were observed, at ___. Exposed nail heads are prone to leaks. Recommend sealing with approved material.” Hope this helps. I see this all the time.
Stu