Back to my earlier point.  Big air tanks in the cargo hold, and pump most of the ship's air into the tanks for storage.  (Run it through a desiccator and a filter, so you don't get anything growing in the tanks.)

Inert gas would make sense for long term storage, but only if you have an bottomless budget and a substantial supply.  (I have no idea how much is available at the local gas giant.).  I would also suggest that N2 would be fine for storage if you wanted to use an inert atmosphere mix.  But inert atmosphere mixes also make it much more dangerous to do anything on board the stored hulks, as any failure of your breathing gear is likely to be fatal.  

Storage with low pressure breathing mix would probably be fine, and while not fabulous to breathe, unlikely to be immediately fatal.  I suspect "minimum survivable breathing mix/pressure" would be the standard storage atmosphere, just to make the job less risky for the yard crews.  

Someone would have to do the risk/reward math, in terms of the benefit of extending the storage life vs. cost of inert storage atmosphere mix vs risk of fatality to yard crews if their breathing gear fails while operating on board the ship.  

Likewise, venting to vacuum for long term storage still means you need to bring air to resupply the ship if you want to put it back in operation.  That may be challenging, particularly for a large ship. Plus, the risks of all the various mechanical problems that vacuum storage may generate.