Just to clarify - an inner container is not what I meant to describe - instead just a panel for each side with foam attached. So when removed you have a set of panels that can just be stacked and take up a fraction of the amount of space.... For single painting crates you shouldn't need 100 crates. You could keep ones in about 10" to 12" increments. For single paintings anyway you could reduce that number that you keep and still save the investment that you have those few.
If you think about it, it does really seem a bit nuts to have to make individual crates for paintings that will be traveling at different times and are only 3 or 4 inches different in size.
I know that is the tradition but I think we are all examining that about now. As long-time exhibition crater there is nothing I have hated more over the years than rehabing old crates, but much of that has to do with the traditional way that interiors were done. Having to scrape out old pads and and such could take forever and was very frustrating.
If stripping the crate just means spending five minutes removing a handful of waferhead screws it kind of puts a different spin on things.
Of course that notion doesn't help you at all with the 100 crates that you already have with traditional interiors that you already have!

I know that your delimma is very common. There is always talk about crate creating co-ops which could maybe work in a museum-dense environment like DC or New York but is harder in the rest of the world.