there is a possibility of rot in the deck and keel to hull joints in any boat with wood in the deck and a bolt on keel. the real question is that the case with a boat you are looking at.
our coronado 41 was neglected for more than ten years before I bought it. the keel was painted with rustolium spray paint and there was standing water in what should have been a dry part of the bilge. the top nuts on the keel bolts were not installed correctly and were in standing water causing corrosion at the threads under the top nuts... luckily the previous owner never put a wrench to the bottom nuts and the threads were fine. I smacked the keel bolts with a hammer and every one sang me a tune. you should do this too.
if the boat you are looking at has any leaks in the deck, you may have rot. the extent of the rot can be discovered by using a hard tappy kind of device (handle of a wood hammer) and start where you know the core is good and move into suspect areas (around deck hardware) if the sound goes from a sharp sound to a dull sound, you have bad core..... I found bad core on my boat around a few stanchions, but it was minor and was easily removed and filled with thickened epoxy. this method is ok for a few square inches, but if it is a few square feet the deck should be opened up and the core replaced.
I know of no other places there would be leaks, the shaft log is solid, the rudder bearing is a huge mound of fiberglass and prop shaft strut should be ok as long as it hasn't had a line wrapped around it and yanked off (pretty easy to discover).
the down points to a coronado 41 is the size of the tanks, 40gal water, 35 gal fuel, and not built with a holding tank. these things are something to overcome. for water, I have installed a dock water fitting in the bow that supplies us with unending water as long as we are connected and we carry a couple of jerry jugs while cruising puget sound. 50 gallons last the two of us about 5-6 days. the fuel we haven't found to inconvenient since we have stayed inside puget sound... with a fuel burn of less than 1gal/hr and time to transit puget sound from end to end being less than 24 hrs we are usually in range of a fuel dock.