about the plastic bag, it depends on the unit but some also have a manual switch on the compressor, once that trips it will not try to restart.
I've never seen controls that will not shut down the compressor on HP. Some will try a couple of restart but that's not going to damage anything.
In most large boats, the water flow stays in the ER... the typical Air Con pump on our hatts pump between 1200 and 1800gph, that's a fraction of the bilge pump capacity you have...
with everything double clamped and inspected, the odds of a leak are near zilch. Even if a hose fail, flow to the compressors will stop and so will the pump. The only risk will be if the leak is in the short section below water line.Then again, if your bilge pumps cant handle that you got more things to worry about. open the strainer with the sea cock open, even a small 2000gph rule will only cycle 50/50
It takes a while to cool the boat on a hot day, electronic incl. TVs, and... dont like heat.
The extra wear and tear on the compressors are minimal since they cycle on and off. on the other end when you come back they will run for an hour or two non stop to get the temp. back down.
Set them slightly higher (high 70s) and enjoy. that's why they're there.
as to growth in the water hoses, I'm not sure flowing water leads to more growth than sitting water.
now if you're going to be going to a long time (weeks...) then you can consider shutting them down, but not for hours.