Are there any application notes or design recommendations for daisy chaining CY7C65630 hubs? For example, connecting four CY7C65630 hubs downstream of a fifth at the board level, making 16 downstream ports available through a single upstream port.
Yes, It is doable.
There is no application note per se for this specific design but it should be just like laying out board for any other USB connection. Even though hub is connected downstream the upstream port of the hub is going to behave just like any other USB device.
So, for example, if the entire device is self-powered, the SELFPWR pin on both the upstream and downstream hubs should be tied high, as if each hub were powered independently of the others?
Yes, see "Figure 5. Sample Schematic for 4-port Self Powered Configuration" of datasheet. Ensure that downstream hubs never drive upstream D+/D- lines before VBUS is active for Upsstream HUB, this is a USB2.0 spec requirement.
If all your hubs are going to be self-powered all the time then yes you can go ahead and tie SELFPWR pin to high.
Could I simply use the PWRn_b outputs of the upstream hub to pull the VBUSPOWER inputs of the downstream hubs high (using a buffer) only when the upstream hub has finished enumerating? This would then be similar to daisy-chaining discrete self- or bus-powered hubs, where the PWRn_b outputs of the upstream hub are used to enable VBUS on downstream ports via a power management chip.
Yep that should work. But if you're going with this hierarchy how will you implement overcurrent protection.