I bought one of these Ultimate Pipe Flashings vent boot flashing units which come with these nail slots to secure the unit. Part of their instructions is to only fasten with nails within the slots designed into the unit.
Lifetime Tool ultimate pipe flashing fitting installation
What I'm curious about is whether or not its a bad idea to nail a vent flashing in areas that are exposed, ie not covered by shingles, even if you caulk the nails.
Nailed Flashing Examples
Here's some examples where I'm seeing them installed with exposed nails.
How to install a pipe boot on your roof
Vent Seal Plus – 2 In. Full Skirt
Perma-Boot 312 2" Repair System – Black
How-To: Shingle around a vent pipe Flashing
Warped Flashing
I would think even with caulking its a bad idea simply with expansion and contraction of the materials at different rates which should wiggle out the nails as I see in my family's roof if you look at the warped and wavy flashings in this image. (I believe all the flashing is original to the roof, so some 40+ years old). I also noticed with the examples that the nails eventually rust and would consequently shrink and allow water to seep as they lose their bite onto the sheathing.
Best Answer
Typically, no. I NEVER nail in an exposed area of a boot, unless I have no choice, which doesn't happen very often.
All nailing in the exposed parts does is create another place for a possible leak. Not to mention, your roof decking swells and contracts with the weather, which means your boots need to be able to move a little as well...