Hi Jessica,

Excellent question. The reasons that artwork are typically not stored in crates are a combination of the reasons you suggest and then the ones that Jamie responded with space, access etc...
Actual storage crates (designed for this purpose) are a whole other animal requiring specialized materials sometimes including things like activated charcoal or corrosion intercept materials. They are very costly and rarely purchased.
If for some reason you do need to make an exception about the only thing you can do is to ventilate the crate to prevent a build up of pollutants. I once came accross a situation where the painting was too big to actually fit into the institution's storage area! in that situation you can open the crate and then close the lid again with small blocks placed in-between the crate body and lid finally covering it with a breathable material to minimize dust. Also less or non sensitive materials like stone sculptures are sometimes stored that way.
Generally though there is a very high level of consensus on this topic. If you have real budget issues "binning" small and medium sized paintings is an underutilized method in my book. That way you can save premium screen space for larger paintings.