Yes, it's safe. The baggage compartment is pressurised to the same altitude as the cabin (usually equivalent to about 8000 ft.), so it's no more risky putting them in your hold baggage than it is risky for the the flight attendant to put them on the beverage cart.
I would be more worried about the knocking about your bags will receive from the automated baggage systems and the baggage (mis-)handlers - this would be a far more likely cause of a soaked suitcase than the pressure difference.