Prepurchase inspection if bad what should I expect to see or what ways to check.

Have it surveyed.

I don't have a boat in mind, Just looking to learn. Could you elaborate a little???

A marine surveyer will check for moisture content in the stringers.

A surveror will use a moisture meter for the transom and stringers.
By the way nice Nova is it a 91?

Moisture content is everything. Wet one's don't dry. Just because it's not soft today, your drives may fall off in 2 years (exxageration for effect)

Most quality boats have enough fiberglass to hide most wood rot- you don't notice it until it's so bad you're starting to see failures. A common one is collapse of the transom- there's no wood to hold the gumbal and transom plate apart so it starts to flex, then leak. Cigarette 35's are notorious for the one tab bolt that screws right into the end of the stringer- if improperly sealed, it will soak the transom and stringer.

I'm thinking that rot is what your looking for? I'm gussing pull a exaust pipe or poke around for soft spots same way on the bottom? Please school me.

Why are boats not all fiberglass so you don't have to worry about that?

Water causes rot. Just because it's not rotten today, that doesn't mean it won't be crumbles in 18 months.

Transoms rot around where they leak- gimbal cutouts and any holes. Somebody mounts a depth finder transducer and doesn't seal the screw- nex thing you know, the transom is soaked and on it's way to rotting. You probably don't see much rot above the waterline unless there's something holding moisture. Lots of old glass cruisers with wood decks and houses rotted at the joints- water would seep in and soak into the wood at the joints.

Some high-end manufacturers build with composites in stringers, bulkheads and transoms. It adds alot of cost and is unnecessary if the boat is constructed properly. The problem usually stems from some DIY guy neglecting to seal a hole. On mid-range and cheapie boats (like Bayliners & Fountains) they just don't give a $hit- the boat will be long out of warranty by the time they rot.