Those hours are not a high, 100-150 is assumed to be standard usage. The one engine is on par, the other is below. I would check to see how extensive the records are on the engines. In general, if they are not serviced when they are supposed to be, I would shy away from them, especially with varying hours like that. If one engine is used more then another, but it was at a low rpm(close to idle), it is not a huge deal, if not I would lean towards saying look for another boat. I believe with the HPDI's, a Yamaha tech can tell how many hours were at low rpm, mid range and high or something of that sort, giving you a good idea of how each engine was ran. If that user was smart and only used one engine at a time, he should have varied which engine he used. I know some guys do slow trolling or may leave an engine idling to keep batteries from dying, or when fishing rips to keep the boat facing into the waves, if that was the case, it was at low rpm's and will not put that much wear on an engine. I've also seen guys who redo drifts using only one engine running at 2500rpm+, that is not good usage and putting more laod on one engine like that will have an negative effect on that engine.
The only way to really tell is to have a tech check the engines, which should really be done before you buy any boat. If you are second guessing yourself, I would follow your gut feeling, unless the deal is just too good to refuse...but then again there may be a reason for that...