In addition to obvious arguments about how it's not about data storage, but transfer, you're also not accounting for the many tiny variations between one item and the next. Items that are stored retain quite a few flags such as whether it's HQ vs NQ on any non gear items, and the person who crafted it, and on gear items there are additional flags such as the spiritbond rate, the repair level, and the many variations to color, as well as the glamour placed over it, and any materia placed in it including what type of materia, if it was a good match for the gear, how many points of what stats said piece of materia offers, ect. While it's true that they could put a simple item number in for every possible variation, that would be a huge waste of resources to do. Even if it's not likely that someone will bond a piece of level 2 craftsmanship materia to a red bunny ear glamoured, level 60 dark knight helmet, that's at exactly 53% spirit bond, and has a repair level of 74%, they'd still have to make a seperate item ID for it if they were to do it as you are suggesting.......
By allowing even slight variations to be retained, they are increasing the data that has to be stored significantly. This is likely why the items that are allowed to be stored in the armory chest are only unique gear that can't be crafted, and that have to be at 100% repair level, as well as why they lose their spiritbond, (and dyes as well I suspect), when you store them. Just claiming that you could "theoretically" make it as low of data consumption as you claim, doesn't mean it would be cost or time efficient to do so for every instance of storage......
Also, I don't know what games you've been playing, but compared to most MMORPGs and even most single player offline RPGs, we have quite a lot of inventory space, as pointed out in the post I'm quoting below.....
EDIT: I would like to correct myself. When I made mention of the armory chest, I was actually talking about the Armoir contained within inn rooms. My apologies for the confusion......