I have the same setup, two D5's and a EK top. As Namron told you, you should be fine controlling them via aquabus with the cable you linked. You can even chain multiple Y cables, just don't overdo it, the length becomes an issue after some point.
I was contemplating the same problem with a lot of USB connections required, especially since I have an older motherboard with only a few internal headers. In the end I decided that I like the flexibility of upgrading the firmware whenever a new one comes out, so I connected both the USB and Aquabus cables to all my Aquacomputer stuff. It is a pain to get to some things and connect the necessary cable after the machine is up and running.
I use a
internal USB hub just for the water cooling stuff and it works great.
Kind regards,
Boris.