G'day
It's a bit hard to explain but the biggest problem is moisture. You can usually find rot by tapping on the transom, paying plenty of attention to any areas where there's any fixtures or screws, listening for a hollow or dull sounds. Also look for cracks, or damage in the gel coat.
There's a book I read called the boat building manual, which goes into everything you'll ever need to know in detail, including identifying problems, or there's heaps on good old google.
Like Huey said you can do most things yourself, with a bit of research and practice. There's a bountiful supply of pre-loved bargains around that could be beautiful again with a bit of hard work.
Cheers Leo