My reason for asking was I use to have a 98 fiberglass boat that had a rotted transom so I sold for a pontoon. Now I am back to fiberglass boats and was just more curious how they are currently made
As time goes on there is less wood in boats. Some manufacturers went wood-free a while ago, but that is not to say that all manufacturers don't use wood.
For those that do use wood they use a rot-resistant wood known as 'KDAT'. Common product names are 'Greenwood XL' and 'Perma Panel'. The change over from plain plywood to KDAT plywood was happening about 20 years ago, so early 2000's.
Since not all boats are made the same, it really depends on what boat and what model year. Of course if you look into the guts of the structure of a boat, you can often tell if there is wood beneath the fiberglass. As a boat ages the wood components often show signs of surface cracks, since the wood often expands as it retains moisture.
Boat companies tend to be vague about the details of their construction and materials, favoring more marketing hype that in reality is not all that significant.
Tell us about the boat in question as that may provide some insight to your question.