I'd worry about it (it's hard not to!) The shading provided by the deck will protect the roofing somewhat, but no roofing is forever, and freeze/thaw on a wet roof takes it's toll over time.
The ideal would have been to add a bit of tapered EPS foam insulation above the roof deck before the roofing went down to provide both drainage and a thermal break over the framing elements, reducing the mold & ice-dam hazard while increasing the energy efficiency. (Dead-flat roofs are a LOUSY idea for residential construction except in arid zones.) Torch-down roofs over EPS foam are common in commercial construction. Tapered EPS is pretty standard too (but can be custom ordered to almost any taper.) Nailer-decks can be applied over the EPS by through-screwing the nailer deck to the structural deck if it needs a bit more substance. Some vendors sell EPS or iso panel products with nailer-deck pre-lamninated onto the insulation.