W wiwb,
All three of these options seem to be addressing basically the same goal….handy storage for smaller items. At most, I would go with one of these options.
None of these options are essential in the sense that anything you could fit in these small areas would likely also fit into the main bag. The question is really if they are worth the weight and complexity for the additional convenience.
I personally haven't used the 'top pockets on the side', but from the looks of it, they appear not ideal for more technical or off-trail hiking. These pockets effectively widen your pack and make it harder to duck under fallen trees etc. Since items in these pockets aren't readily accessible when you are wearing the pack, I would opt to skip these and just put the stuff inside the main bag.
Hipbelt pockets can be really handy if you have some smaller items that you frequently utilize while hiking (ie. camera, water purification etc). I do find these handy for my camera and water tablets, but I like the hipbelt pockets to be quite small. If they are bulky then you can wind up hitting them on stuff or hitting them with your arms when you walk. IMO, the Zpacks ones are a little big at 1 liter each. Most hipbelt pockets from other brands are about half that. If you're never used hipbelt pockets before, then you probably don't need to start using big ones like this. If the pockets are too big then they become a 'catch all' for your small misc. gear and then you start needing to empty out the pocket just to find what you're looking for.
To me, the shoulder strap pockets look to be the best of the three options. The size is more reasonable and you're right that you could carry water here to move your center of gravity slightly further forward, which would mean a we bit less forward lean when hiking (ie. the Aarn idea). This effect would be pretty small with just 2 x 0.5L of water, but it can't hurt. On the downside, if you weren't going to get daisy chains, now you need to add them so you can use these pockets. The weight and complexity can add up. You might be able to cancel this out by omitting the side pockets. You could skip the side pockets and carry 2 x 0.5L in these front pockets and then if needed carry a bladder in the main bag for additional water capacity. This would save weight overall, but if you don't like having the water bottles on your chest then you're kinda screwed if you omit the side pockets also. You also wouldn't have place for your alcohol bottle, and these shoulder pockets wouldn't be that useful for other stuff if you have them filled with water bottles all the time.
I personally decided to keep things more simple and go with none of these options. I can use my pants pockets for my camera and water tablets. I don't need a pack cover handy since I'll seam seal the pack so it's waterproof. Everything else can go in the pack. If you start to have too many options for putting stuff, then you'll forget where you put it. A bit of small stuff storage is nice, so the shoulder pockets are decent way to go. I kinda wish Zpacks offered much smaller hipbelt pockets. You could contact Joe and ask for some. Joe's pockets are 1L in size and I find my 0.5L hipbelt pockets on my ULA pack to be plenty big.
BTW: My Zpacks Zero shipped out Tuesday! I'm excited to get it, even though I'm not sure I'll be able to use it for a while. Winter is in full swing here.