What you see is common practice. It's easier to put new plywood over old, than to remove the wood down to the rafters. When we have to resheath, we try to sell the removal of the old plywood precisely because of what you noted - anyone in the attic won't see the new wood, they will be looking at the old. Some homeowners don't want to pay the money to do this, but usually we are able to persuade them to do the job properly. But then again, most of our customers are buying the quality, not the price.

Practically speaking, if your roof is well ventilated, then the old wood will eventually dry out and there should be no problems with fungus or mold already present in the old wood. However if your ventilation is not good, then the old covering has the "mold-starter" built in, and condensation in the poorly-ventilated attic could cause more damage.