Yes, water in the holes. Wax will normally stop it, but there are never any guarantees. Just had the same problem myself on a guitar body around the pot holes (that should have been well sealed at the edges with paint by now).
I'd get a very small drill bit and drill a small hole in the finish at the very end of each crack, which should stop the cracks expanding further, especially if they want to run out from under the neck plate.
I must say that none of my six Gibsons has ever showed any signs of finish cracking, but two of my Fender Strats had the ubiquitous lower pocket edge crack appear over time.
But a lovely smooth and very shiny finish. I feel your pain with the cracks.






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