I currently do the same thing you do except I try to keep some tissue or cotton between the flowers for extra protection. I think it's a pretty good idea if you don't have a lot of storage room because the small plastic containers and be stacked on top of each other, not taking up very much room. Just label them and keep like flowers together so you can find them easily.
Pizza boxes? Maybe that will work? It's something I have wanted to try for a while. For now I just keep them in a plastic container too. I need to get some pizza boxes!
The plastic storage units with drawers that you can get at Wal-Mart are very good for this. Put a layer of non-slip plastic on the bottom of each drawer, so your flowers won't bump into each other or the sides of the drawers and break.
I keep mine in cardboard shoe boxes, easy to stack, and light cannot get in to fade the flowers.
I find the best way to store gumpaste flowers is in cardboard boxes/pizza boxes - anything that is a clean cardboard box. if you put them in sealed plastic boxes the air doesn't circulate and the flowers have a tendency to become soft again as you are sealing in the air. I lay them on some sponge/kitchen paper or bubble wrap is another great thing to add some cushioning. If you have wired flowers I often put a large piece of polystyrene (or styro foam?) in the bottom of a cake box and then you can stick them all in upright and fit loads in and just pop the lid on. its a great way to use up any slightly damaged cake boxes
hope this helps
I use plastic containers once the items are totally bone dry...cardboard if notand then transfer to the sealed plastic.
If your stuff isn't totally dry then yeah sealing it up will keep them soft. However if you live somewhere prone to periods of high humidity, storing it in a cake box will allow the wet air to infiltrate and cause drooping while if you've stored them in an air tight container it keeps the wet air out.
Just a tip from a personal experience. A sachet of silica gel in the plastic container will help as well.