I think a solution might be somewhat similar to something Blade & Soul did. You have a separate wardrobe that can store outfits, thus alleviating a spot in your inventory. So for FFXIV, I'd suggest the very same, with it being able to store your glamour pieces. That, or simply being able to toss the item once its appearance is glamoured onto another would go a long way to helping storage without overloading the servers. In fact, the latter wouldn't even touch them at all. I have Lady Clogs and Amatsu Haidate glamoured for my craft set-- with both of those items stuffed right back into the armoire.

Unfortunately, I don't see them changing much, what with this effectively limiting the number of retainers people will purchase. Granted, a work around to this is leveling an alt and asking to use your Free Company's chest to swap items from time to time.