The only con/issue that comes to mind is that there's no "one-click" way of splitting an existing pool into two pools let alone into a pool of two pools.
If you stick to using the GUI, you have to remove half your drives (problematic if your pool is over half full!), create a new pool using them, then create the new super pool that adds the other two pools, then transfer all your content from the original pool into the super pool (which, because the pools are separate drives as far as Windows is concerned, involves the slow copy-across-drives-then-delete-original process rather than the fast moving-within-a-drive process). But if you don't mind the wait involved in basically emptying half of the drives into the other half and then filling them back up again, it is definitely the simplest procedure.
Alternatively, if you're comfortable "opening the hood" and messing with hidden folders, you can manually seed the super pool instead - it is much quicker but also more fiddly (and thus a risk of making mistakes).
Note also that nested duplication is multiplicative; if the super pool folder that will show up in your hub pools when setting per-folder duplication is x2 and your super pool is itself x2, your total duplication of files in the super pool will be x4. So I'd suggest setting each hub pool's super pool folder to x1, setting the super pool itself to x2 and only then commencing the transfer of your content from the hub pools to the super pool. I hope that makes sense.