The engine in and of itself is not a bad engine. The 210hp versions are great. They don't have after coolers or fuel coolers and they are not "squeezed" so hard. Your current engine is rated at 330hp and is only 360 cubic inches.
None of this really has much to do with my view of them. Bottom line, you go look at boats on YW. It is VERY common to see Cummins powered boats where one out of the two engines has been rebuilt/replaced. It just seems that all of the "peripherals" on the engine were not engineered that well and while, cheap, they can do some very expensive damage. And that is what seems to happen. That and the fact that they are extremely sensitive to being overpropped/loaded. These two things are the biggest reasons why they don't last. I bought my boat with 350 hours on it. I figured I got to them before any damage could have occurred. And I was mostly right.....BUT....I had a fuel cooler fail and have been chasing my tail ever since. Injectors on the STBD engine got trashed. I finally got that squared away. Now I have a smoke issue on the PORT engine where I have adjusted the valves and changed the injectors....to no avail. It smokes pretty heavily on start up(white unatomized fuel...slick on water)....and clears up quite quickly and virtually smokeless after that. Which tells me it might be a ring sticking on start up. I have not thrown it out to the boat diesel crowd but I am going to today.
My point here is one of the reasons I like diesel engines on boats is you can work them very hard and generally not have to worry about them. That does not seem to be the case with the Cummins. I have yet to have any carefree operation out of them yet. It just seems something is always needing attention and it seems I feel the need to baby them....all qualities of a gas engine. My last boat was Yanmar powered. 4LHA-STP....240hp with only 213CID!!!! SO it was squeezed even harder and I ran it hard. BUT.....not a single solitary hiccup in the 1000 hours that I operated it. And the people that know Yanmars say the 4LHA is one of the best Yanmars in the bunch. Anyway, given the choice in a planing or semi planing boat, I would choose Yanmar over Cummins every time.
Another thing, and this is total conjecture on my part. Cummins really are good engines at their core. So good they seem to chug along happily even when something is wrong...masking whatever it is. So when you think something is wrong or just think something is not right...a small symptom that you are inclined to "blow off"....DON'T!!! It is trying to tell you something.
Your engine will do you just fine in your installation because you don't run it hard(my assumption). My guess is you run it in the upper teens. It will last 100 years at that power setting. But I would get a stategy for your aftercoolers(which I think you have done) and your fuel coolers. Your fuel coolers will **** your world if they fail. They have mine. Tony Athens pretty much says to just remove/bypass them. Easy to say when the highs in the heat of the Summer where y'all live might reach the upper 70s while soaking in 50-60 degree water. My strategy is to replace them every 2 or 4 years. The Cummins price is $190 per. I buy mine from Tony at $85 per cooler...because he has piles of them that he takes off of brand new engines. Anyway, $170 every 2 years is pretty cheap insurance and what I feel is good enough risk mitigation.