if its been run for a long time, like a long time, the strut bushing will be hammered out and need to be replaced. If it's been abused extensivly, the next bearing to go will be the rear output bearing of the transmission. You will be able to tell if its bad, simply open the engine box and try to shake the driveshaft up and down. If it feels like it is moving in your hands and makes a small click sound, I would take it to a dealer and have them measure the runout on the shaft with a dial indicator. That will tell you exactly how worn the output bearing is. Worn bearing = iron filings in the oil. I would follow the dealers recommendations at that point. OR, you could call them and get the spec, and measure it yourself. If the shaft deflection is within spec, you should be fine. It will only move 0.001" to 0.003" or so, a very small amount, verify that specification prior to measuring. Measure carefully.
The harmonics generated by bent props and drive shafts vibrate all the way thru the transmission and into the engine crankshaft, If it shakes the whole boat, just imagine the sideloads placed on all the intrenal bearings, it can be upwards of hundreds, maybe thousands of pounds force when its out of balance. They should be repaired immediately, even if you have to stop using your boat for awhile.