I have a pair of 2003 HPDI 250's and I write on here pretty often about the HPDI's and DIY stuff to keep them running well. Everything from the DIY--low pressure filters, VST, and the tiny filters on the High Pressure pumps. I have about 1,000 hours on mine and they run flawlessly. The key has been an aggressive maintenance schedule. I replace all of my filters twice as often as recommended. Once you learn to do them yourself, you realize that you are not only saving $100's in mechanic bills, but extending the life of the motors. You are also making it safer for yourself to take extended trips offshore. I go to the Bahamas, the keys, and Dry Tortugas pretty regularly. I have never had an issue. Unlike the 200HPDI's, the bigger block HPDI's (250-300) have a very bad reputation and rightfully so. The average boater does not know how to turn a wrench, and certainly does not want to. The majority of all the problems have very simple solutions--------THEY REQUIRE VERY CLEAN FUEL!!!!! Because the motors have a very bad reputation, you have a very good weapon for negotiating a good deal on them. But make sure they have all the updates from Yamaha, and do a full compression check and inspection of them.
I see it this way, you have a choice: You can run away from these motors and follow the hype; or you can pick one up for dirt cheap, add a 2 micron water separator, run non-ethanol fuel, and replace your filters aggressively and they will run as long as mine and hopefully longer.