Have you seen this for yourself ? Should be easy to tell if chewed through, broken by wind, broken by flying branch, or punched through by a contractor trying to create more work.
I suppose a squirrel could chew through some of the light-gage aluminum on the market these days if he was really frantic, but only if he/she had a nest or nut cache inside and had the normal access hole blocked, or was trapped inside. I find it hard to conceie of, but I have seen squirrels and rats chew through thick fiberglass housings, so maybe so.
The other possibility is he meant the rubber collar on the roof jacks (that keep water from running down the outside of the pipes into the attic), which rodents will chew on - if that is the case, the damaged rubber needs replacing (which normally means the whole roof jack), and then a metal protector collar (stock item) slipped down over it and decured over it. Cost probably about $100-150 labor and roof jack and collar, about $50-75 additional per additional one needing replacement (may be 2-5 on a roof, typically).
If you find the metal was truly chewed through, replace above-roof part with galvanized steel - no way a squirrel can chew through that. Probably about $100-150 cost by a roofer or HVAC contractor, assuming this is a pipe or bathroom or kitchen vent rather than the furnace. If furnace one, probably $50-100 more for materials.