No, I leave all mine set up. Sounds a pain to disassemble and reassemble everything constantly 
What about some stackable storage boxes though? In the UK we have a brand called Really Useful Box which are good quality, various sizes and have good closing lids (strong clips). You can get various colours instead of clear so it looks less cluttered if they are stacked in sight in your room (black = not see-through for example) but they are quite expensive for a bit of plastic, lol.
You can get bespoke dust covers for the Honeycomb gear (check eBay) but not seen bespoke hard storage just for those things.