We did an estimate once based on independent dojo student numbers and figured there were as many people training in independent dojos in Victoria as there were in the affiliated organisations. That was a 10 years ago and I have since moved to another country so am a bit out of touch but it probably hasn't changed very much.
Hmmm. That sound VERY familiar! Here in the UK there is a rainbow array of more than forty organisations, some affiliated to their respective hombu, some that have been independent for decades, and some with affiliation via an overseas organisation. It's sobering to realise that this is a global and inevitable tendency. The only exception I can think of is France, where there are legal requirements for teaching qualifications, which has tended to keep the number of separate factions low.