It's not exactly intended to be used for THAT much storage. If you are at the point where a large quantity of minecart chests like that would be necessary for any sort of item, I would recommend actually using those items to achieve something or give them away to someone else who will use them to achieve something.
If you're THAT paranoid about people stealing from this sort of thing (joke's on them, they just took a ton of what is likely to be a cheap and abundant resource that to you should be able to easily replenish) then surround the thing in blocks and use signs to ensure that no one can even break in and access the minecart chests, let alone destroy them.
Also, I posted this in the "Everything Else" section for a specific reason. It's not really intended for the server but for MC gameplay in general. If it were server specific, I'd post it in a server specific section.
Lag can certainly be an issue so I am going to assume that people are smart enough to know what is and isn't reasonable with using this. I just posted the idea. If someone abuses it, the damage they do is their fault, not mine.