The preferred method is a combination of tapping and a moisture meter. Tapping is best done with a leather tipped hammer ( not so common) or a plastic faced hammer (easy to find). You don't want to use a standard big metal faced hammer.
Rot when it gets bad will result in delamination of the fiberglass from the core. When that happens, the tapping sound will sound hollow and/or dull. When there is no delamination, the taps are kind of sharp(solid) sounding.
Examine the outer side and as much of the inner as you can see to look for stress cracks. Some cracking can be normal and not an issue but bigger cracks or areas when the two sides of the cracks are at different levels may be a sign that things are flexing or swollen.
The moisture meter is the definitive test butit is only as good as the skill of the person using it. High moisture readings can be bad signs or just an indication of a small condition than can easily be addressed such as seepage around screws , garboard drain and the like. To properly do a moisture check of the transom and hull while you are at it, the boat has to be hauled and the hull has to be relatively dry. You can't do those test in the rain

Note that some models will have excessive moisture in some area and a good surveyor will know those cases.
I know a lot of folks suggest you put a load on the transom and then kind of bounce the motor up and down from the prop end to look for flexing of the transom. The only time I saw someone do that and see motion was an old hull that had serious cracks AND had a steel plate bolted to the transom to stiffen it.In other words it was pretty obvious before the test that the transom was in bad shape.
I feel that if the transom flexes under load, there will be cracks, stress or spider that tell you something is not right.