Seems like this topic-old vs. new engines comes up on a regular basis. And the discussion always seems to revolve around the same circumstance-newere engines need power to run so no power-no run or a lightning strike will fry all the electronics and again no power-no run.
Since we have JD 6068 TFMs, obviously fully electronic and turbo'ed, some time ago I spent some time talking to my friendly JD guy here in Seattle and to an acquaintance at Northern Lights. Both were enlightening conversations. On the general proposition that electronically controlled diesels need electricity to run, it was pointed out to me that the electric system on the engine is completely self contained within the engine system. That is, the initial power on start comes from the start battery and once running, power comes from the alternator. So failure, even total failure, of an onboard electrical system will not affect engine operation. Of course a dead alternator or totally dead start battery with no alternative could be fatal. But those are normally resolvable and have nothing to do with the question at hand. So, I don't consider electrical failure as a substantial reason to discount modern engines.
On the ECM, of course there are and have been ECM failures. According to my JD guy, these just do not happen very often and when they do it is often a programming failure or a circuit board failure, both of which tend to show themselves early in an engine's life. As to lightning, forgetting for the moment the very small probability of an actual strike, if lightning does stike a boat and does go to ground through the engine, the ECM is protected by being isolated in a separate metal box that is separately grounded. In fact, according to JD, ECMs are almost never affected by lightning. But what can be affected are the multiple sensors on the engine, some 12-15 that send info to the ECM to control the engine. Almost all the engine failures from lightning are because the sensors are fried, not the ECM. Now as it happens, JD recognized this. So, the ECM is programmed first to find alternative sensor sources for needed information. Failing this, even if all sensors are failed, the ECM is programmed with a basic "get home" operation mode. So, the engine will still run, maybe not at max, maybe not as efficiently or effectively, but it will still run. According to my JD and my NL friends, almost all ECM controlled engines have this feature programmed in.
As to lightning in general, as best as I can find stats, the most likely to be hit is a sailboat (duh-the mast!) and the second most likely is a sportfisher (again Duh-the tower and outriggers). Trawler types rank pretty low on the list. And overall, the probability ranks close to being an irrelevant consideration.
As to reliability between old mechanical and newer electronically controlled, JD at least says that their history and studies show a greater reliability with newer engines. Better initial construction and design, modern alloys etc, better and more efficient control through the ECM created less stress on individual parts, the info provided by the ECM provides far better and more timely information on operating conditions and status of internal parts. If monitored correctly, potential problems can be identified and rectified before failures. I think this shows in the generally increased maintenance intervals on newer engines. Of course, there are always the outlier anecdotes, someone's engine fried by lightning, someone's turbo blows, or whatever. But are these incidences, even if actually verified, occurring often enough to justify ditching the engines? To me it is not even a consideration. I simply would not consider an old engine over a newer one. And I would never consider replacing our JDs.