Thanks for both of your inputs, it really has been a help. I am going to buy a few bits to get my case finalised so this can include fans if needed.
I am sure the OPT header is sending out a PWM signal, I would expect it to as I have always run 2 CPU cooling fans and one has always been plugged into the CPU fan header and the other into the CPU OPT header and they speed up and down in unison.
I might just bite the bullet and plug both CPU cooling fans back into their old headers and plug all the case fans through the hub and into a 4 pin chassis fan header. As long as it is quiet when idle and I can hide all my cables it is all I want really and was the main purpose of the hub, though it does without doubt lower the ambient noise in the case when idle which is an added bonus. It is silent at idle which was not the case before.
Alternately I can just swop out my 2x 4 pin CPU fans for 3 pin fans and then have all the fans running through the hub into the main CPU fan connector, though this will cost more money and I am really not sure if that is to be trusted as 3 pin fans are not really meant to be variable are they not?
*edit* I have a couple of brand new Corsair 3 pin 120mm fans at home somewhere though think they might be more aimed at case cooling than CPU cooling.