I am running twin Tier 2 John Deere 6068's, turbo but no aftercooler, with 201 HP each. The dealer and the factory manual both made it clear that the extended run-in period, using their break-in oil, was critical to the life of the engines. Essentially, and from memory, it was to run the engines at 60-80% load for the first 100 hours. Obviously some time at higher loads and some at less was OK, but it was key to avoid idling as much as possible. After the first 100 hours and normal oil was installed then there are no real limits on running them slow or lightly loaded. No need for end of day high power burst, but no harm doing it either.
I find myself typically running in the 30-40% engine load range, because that's all the boat needs to cruise at good speeds. Perhaps more lightly loaded than ideal but purring very economically. The engines are downsized from the ones I replaced and I can no longer get to 16 kn, which is fine by me. I didn't like the gph burn at 16 kn, and it really needed more power (and even higher gph burn) than was originally installed to get beyond the 'semi-planing' (= 'ploughing'/humongous wake) 16 kn scenario. It would probably take at least 800 HP for that, which I would hardly ever have used.
Now its a different situation if you buy the boat with all that HP installed. My take is that if a modern engine was run-in correctly then using it lightly loaded will be fine. Info from experienced posters above support this. The difficulty with a used boat, in relation to their engines in particular, is knowing how they were treated in the first 100 hours. Dealers may be able to plug into the ECU and tell you quite a lot though. That first 100 hours did seem to be a long time, and I'm glad I got it done in the first decent cruise to Desolation Sound etc.
Although my boat ex: factory was claimed to be 48,000 lb, its a bit over 60,000 lb now (mid-load condition). The size and weight bring comforts, I sacrificed speed because I'm a cheapskate regarding visits to the fuel dock.
Advice to the OP to first find the boat that fits, and look and engines and other things second makes sense to me. If there is an occasional 'need for speed' feeling then stay under about 40' and look for a relatively light weight, and then the fuel-dock pain won't be too severe.