For posterity, I found what the issue was:
The network cable between the two CDJs was unplugged. Once they were connected both players then appeared in Rekordbox.
I have two CDJ3000 connected to a Macbook via a USB3 hub but cannot get them both to appear in rekordbox at the same time using LINK in Rekordbox.
If I unplug the USB on Deck 1, Deck 2 will appear. If I unplug Deck 2, Deck 1 will appear - but they won't both show at the same time?!
They both show up in the sound settings, so am I missing a setting or something else here?
It's not the hub nor the cables, as I've tried the connection with other cables and hubs and it produces the same behaviour and they are both recognised on the laptop just not in the software.

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For posterity, I found what the issue was:
The network cable between the two CDJs was unplugged. Once they were connected both players then appeared in Rekordbox.
For future, try just one CDJ via USB, then link the two via ethernet.