For the ship itself (as opposed to cargo or supplies, which will likely be a mess unless they're in sturdy air-tight containers), my guess is that this depends on the type of ship - I'd expect a military craft or a paramilitary craft like a Type S Scout to be completely fine, and just require a good cleaning and a refresh of the life support system, since my guess is such ships are designed to suffer minimal effects from vacuum. OTOH, a civilian vessel would likely not be built to handle short-term vacuum exposure and might well require some major refits of furnishings, and perhaps more serious damage.
