PCBgogo

There are clear jelly like (2 component) potting compounds which are easy to remove if needed.
These are often used in hybrid modules and Dave told something about them (including their name) in a teardown of a cypress AAD (Automatic activation Device (for the reserve parachute)) .
Anoter way would be to remove the connectors from the equasion.
Either solder wires directly between the boards or solder a piece of flex between the boards.
Some board houses can make a combination of flex and rigid in a single pcb and these can be folded.
If your pcb does not generate much heat (power) you could put it in a plastic bag and top it off with silica gel.
Completely hermetic rigid enclosures are problematic because air expands and contracts with temperature changes which will cause pressure differences. A bladder can be added to allow for this expanion/contraction.
In industrial settings it is (was?) common to add a heater to scare away condensation.
You might be able to protect connectors with application of vaseline, silicone grease or similar.
The contacts will push the grease away and still make contact, but moisture has no chance to get to the metal.
Using connectors that simply do not rust may be an option.
For example: Car trailers have used brass contacts for ages, and those connectors are out and unprotected in all weather.