Just finally getting time to do wiring on Root 3 CNC and noticed the Panel seems to accomodate a D9 connector which has not enough terminals for 6 end stops including ground each.
But seeing as they all share a ground back at the board, is there any reason why I can’t just have one ground on the connector and split it up at the machine end?
You are correct - they can share a common ground 
Check this out for more information - you might find it useful
Oh nice, the wiki lives!
As it turns out, the controller I’m using (or rather RepRap firmware) only allows one end stop per axis anyways so I can only use 3, with the max extents set in software.
Which board are you using - bit surprised would be limited to one endstop per axis?
Well technically one per motor, but in affect with axis soft limits, one end stop per axis is working out just fine.
Using Duet board. Its really for 3D printers but with a but of tinerking it can work and and It has some nice perks (like the PanelDue touch screen).
Not as nice as Pete’s but his didnt exist yet when built/ordered everything.
Can you fix that link please 