Should You Exercise The Kids

If / when I'm dock bound I like to give them a quick run every few weeks or at least once a month. As much to circulate some oil on the bearings and flex the raw water impellers so they don't take a set.

That's a good start, but I'd get the boat off the dock and put through its paces for a half hour or so at least once a month.

People in the north leave Diesel engines sitting all winter on a regular basis. I wouldn't worry too much about it.

I agree. Put a load on them for a brief run if possible. Just running them without a load could create wet stacking. On the other side, run the block heaters all the time and let them sit. This is done in many place without issues for a few months.

I semi-agree about the diesels, except that the boat isn't up north where winters are dry and not much grows in the winter water. When damp air is introduced to a motor I like metal kept lubricated. I'm also concerned with other systems from growth on the bottom and running gear to shaft logs and a/c's and plumbing. An alternative would be to winterize the boat.

Let me say this... when I pull into Ft. Lauderdale for our annual yard period, I never do anything other than shut down the engines and leave them until we are ready to use them again. I've never once had a problem.
To the OP- I wouldn't overthink it.

Whatever works for you is great, but I've run into all sorts of gremlins on boats that sit for long periods from farms growing on the bottoms and intakes to dried seals and gaskets to damage from electrolysis to varmints setting up homes and eating their ways to them. How not running the diesels will affect their longevity I DK. That's why I say I semi-agree with you on that, but I just don't feel it's healthy to leave any motor for long periods with all the lubrication sitting in the pan and the cams not moving.

A lot depends on what kind of exhaust the engines have and the potential for condensation in the exhaust system. The most compelling issue is that there are always open or partially open exhaust valves when the engines are stopped. The concern is that cylinder walls can corrode over time if the engines aren't run. Although the engines won't come up to thermostat temperature, running one engine in reverse gear and the other in forward brings the temp up a little higher. Doing that for 15 minutes or so every two weeks has worked for me on a pair of Cat 3406's over 5 years. A run up in RPM in neutral to finish has been my practice. It may be arguable whether or not there's potential for damage if it's not done, but I've experienced no ill effects. A friend that manages a number of dock queens has been doing it for years as a regular practice on his fleet.
Another possibility is rubber vanes in a raw water pump taking a set in the area of the cam plate and causing a "flat spot" on the impeller, reducing the effective output of the pump.

I don't disagree that this is a good practice for dock queens. Perhaps I misunderstood, but it seems like the OP is going to be away for a couple of months and is wondering if someone should be running the engines while he is. If the boat is regularly exercised (other than this couple of months) I don't see an issue. If the extended absences are regular, then I would concur that hiring someone to start the engines (and perform other duties, for that matter) would be worthwhile.

No expert but mine sit winterized (antifreeze in place of saltwater) and idle on the hard for 6mos as most do here in winter. Can't image it's much of an issue. And if you think winter in RI is dry, you haven't been. It's a wet, mostly rainy, cold mess.

What kind of use the boat normally gets, what kind of boat it is and what exactly the OP means by "a few months" would be very relevant questions.

+1 on what Capt. J wrote. When I looked for boats for clients I always cautioned that too few hours are as bad as too many. I like to see 100 to 200 hours per year.
If you can't get it off the dock you can't. We all do what we can do. What you propose sounds fine. J takes care of a bunch of boats. Doing what he advises in your slip is good. One thing I will add though is to put on some extra lines. Good in case a storm comes up and good for safely exercising your motors.

Capt J, what's a dead hole?

Bad cylinder / piston, etc.

I do not mean to hijack this thread, but, I keeping reading about not getting up to temp. I must be an anomaly (no comments, please) Man 820's freshwater cooled. I store in the water on Long Island. This year going to Beaufort NC. I start the engines. Fast idle at 750 rpm until the temp gauges move. Slowly raise to 12oo rpm as it reaches 170-80. Takes a while, but isn't that "coming up to temp." Also, with my kind of HP I am not putting them in gear for any length of time while tied to the dock, but I do give them a bump in and out of forward and reverse to exercise everything. I do not follow this procedure once I'm winterized in late December. I just let every thing sit with plastic bags over my airseps, my air box stuffed, my engine heaters on, and every once in a while maybe half a revolution on the engines to changes the valves. The engine heaters keep that engine room and equipment above 45 (?) even on the coldest days. I can rummage down there with just a shirt on. I only winterize in case of a power failure.

Sure you can ignore them and get away with it but is that proper care? No.
Block heaters should be on
Start them every 3 weeks
ideally get away from the dock and load them up.