In my opinion, it really depends on how your teacher teaches.
I haven't had separate books for notes and work for science this year, because my chem and physics teachers gives us our notes already printed in booklets which we go through and annotate and fill in while they teach. I think most VCE teachers are the same, because it saves time. I agree with you for maths however, definitely separate books are good. One of my friends had books for notes and work at the start of the year for chem and physics, but her notes ones are practically empty because we only really write notes in the printed booklets in class.
If you want to write your own notes out, definitely use a new fresh notebook though. I started writing notes for bio, chem, and physics, and you'll want them in a separate book if you do that.