Only one extension subject would count towards your ATAR, but it is possible to be enrolled in more than one.
Note: Only one Higher Education Study may contribute towards satisfactory completion for the award of the VCE.
The VCAA Handbook states that only one Higher Education Study may count towards satisfactory completion of the VCE. Similarly, only one Higher Education Study may contribute to your ATAR.
Whether a university permits you to be enrolled in more than one of its extension subjects would be a matter of university policy.
For example, University of Melbourne:
No. The Extension Program is designed to be taken alongside a full VCE workload. To study more than one subject area at a time would be unmanageable for most students and would compromise the aims of the Program.
It is possible to enrol concurrently in extension programs of different universities, as far as I know.