So I have recently answered my own question (just kidding, contacted the foundry) and here's the solution. Currently you have to set this at creation time.
example:
shuffleDiffA = nuke.createNode('Shuffle', 'in DiffuseDirect', inpanel = False)
According to nuke the next release will allow you to set this option more like you would any other knob.
--------------------------------------EDIT--------------------------------------------------
I've been trying to write some python scripts for some co-workers in nuke. This is my first time in nuke and I'm kinda hating the documentation haha.
So I'm doing something simple like reading in a frame range (no problem), attaching a shuffle (again no problem), and then I need to switch the knob 'in' to a different value.
so...
rCustom = nuke.Read('file{'+customPath+'}')
setfile=rCustom.knob ('file')
setfile.setValue(customPath)
shuffleDiffA = nuke.createNode('Shuffle')
shuffleDiffA.setInput(1, rCustom)
print shuffleDiffA.knob('in').value()
# Result: 1.0
Now if I attempt to shuffleDiffA.knob('in').setValue(12.0) #Yes 12.0 is the number I need
No change happens and it does a #Result: False
Any ideas on how to change this value anyone??