If it is apples to apples and you are confident on the condition of the used machine there I say go with used. Two years down the road you won't know the difference from one to the other and you'll have saved a bundle.
Then I've always leaned towards used machinery as an economic alternative. But then I also enjoy learning the mechanics, operation and maintenance of a used machine and bringing it up to spec.
As to software etc. I've never considered CNC control software updates to be important other than to fix problems. CNC's are XYZ movement contraptions and making a machine move in 3 directions is not very complex in the computer world. It the control software worked when the machine was new it will continue to work until the machine is worn out.
If there is more to the software than just controlling the machine movement, and you are using those features, then an upgraded version could be very helpful. Since I do all my pre-control software work in AutoCAD and Enroute those are the software packages I might consider upgrading. There is no reason to upgrade my WinCNC control software to a more current version though.
BH Davis