I built a general stockpile in the main spire. All the chests are single and reinforced with emerald. Meaning, someone with a diamond axe will take several minutes to crack one open. Once I get more emeralds I will expand the stockpile, hopefully to at least a hundred single chests.
Here are the reasons I did it this way:
1: People with x-ray will be able to see chests through walls. So hiding them is pointless. We also need to have access to them, which means if the information gets out for any reason we lose that layer of security.
2: Creating a Citadel'd room takes a lot of resources if it's anything more than Stone, and a Stone reinforcement will keep out an intruder only for a short time and will not deter him at all. Once someone accidentally leaves the door open, or the intruder cracks through two Stone-reinforced wall blocks, we lose that layer of security.
3: Cracking open Emerald-reinforced chests takes a LONG time even with a diamond axe. One cracked chest doesn't reduce the effectiveness of the other chests' reinforcements.
4: An intruder will make a cost-benefit determination based on time it takes to crack a chest vs. what he will get out of it. If he knows there's diamond, emerald, etc. in the chest he will take the time even if it's Emerald-reinforced. But if he's presented with a huge room full of single chests, all warded up with Emerald, he knows not all of them are going to pay off. Assuming that only 1/10th of the chests will hold something worth his time, he's faced with the prospect of cracking chest after chest full of nothing but dirt, seeds, half-dead stone picks, cobble stairs, and other worthless shit - and maybe there isn't even anything good in this room at all! Maybe it's a ruse and all the best loot is hidden elsewhere!
Here's what we need to do, banding together as a fort, to make sure the storage remains secure:
Keep the storage tidy. I know a lot of dwarves like to come home, empty their inventory into the nearest chest, eat a mushroom, and log out. Don't do that. Your friends won't use the stockpile unless they can reliably remember what chests hold what things. If you must do a dump chest, at least use an empty stockpile chest - that way it's not clogging up a working chest.
Don't leave intruders information that helps them figure out what is in each chest. Don't create any patterns in chest contents. Don't put all the crap blocks on the lower layer, or all in one chest stack, or along one wall, etc. Similarly, don't put down any signs identifying chest contents. Even obfuscation! The goal is to demoralize the intruder with the effort:reward in his head, and if he thinks there will be diamonds in a chest he will probably crack the chest. Once he realizes the good signs have crap in them, he thinks maybe the bad signs have goodies in them. Regardless, he's encouraged to crack more chests than he would with no info.
Don't store anything worth anything outside the stockpile. I know a lot of dwarves like to keep materials near where they will be used. Don't do that. Take the extra effort to travel between the stockpile and your work site. Anything left outside the stockpile will probably be stolen.
Don't put down double chests. I made sure there isn't an exploit where you can put down a second chest to un-reinforce the first one. Instead the reinforcement spreads to the double chest. So someone could grief us by coming in and dropping a bunch of extra chests and making the room ugly. But the reason I built the room with single chests is to maximize the amount of effort someone has to go through to crack the whole room. Yes there's a legitimate complaint that, for example, we will need multiple chests for stone (and don't use two adjacent chests!). That's the primary component of the security system. Yes double chests are convenient for us. They are also convenient for those bastards who would like to rob us blind.
Try to put your trust in the stockpile. We're going to succeed more if we pool resources and get those higher-level factories up and running.
While you'r doing renovations, you might discover a chest embedded in a wall or floor, warded with Emerald. And you might wonder why there's nothing in it. These are intended to distract and waste the time and effort of x-ray abusers. Please leave them. If you break the reinforced block you don't always get the reinforcing material back.