A lot of the military stuff is fitted into very light and strong hermetically sealed enclosures, and pressurized with dry nitrogen. That solves all of the environmental and heat dissipation problems. Its obviously completely waterproof that way as well.
Conformal coatings are horrible things to work with, just about impossible to fault find, because you cannot probe the boards with a multimeter or oscilloscope. Everything is covered with insulated glop.
Even worse if you need to replace a component.
If I had to do something like this this myself, I would fill the thing right up with oil.
That ends up being far too heavy for most militay applications, but its used a lot in safety critical equipment used in deep mining applications, where total flooding is far from unknown.
Substation transformers operating at extremely high voltages also use oil filling for both cooling and insulation.
It can work for you too.
If this is going to be a "do it yourself" project, oil is probably the simplest and easiest solution to your problem.