Only if they admitted to doing it… The Access and Disrupt bill isn’t actually to do with evidence gathering. The way I see it happening is one agency would come up with a cover reason to hack you under that bill, which you or even other parts of the Government like the public prosecutor wouldn’t ever know about (it’s secret and there’s no obligation to inform anybody).
As far as most people would be able to tell, the Federal Police would have just raided you on an anonymous tip, seized your computers and found material you never knew was there…
It’s still heinous misconduct, but they’ve legalised 80% of the process and the level of secrecy around these agencies is so ridiculously high and the accountability so low, so it’s a lot less of a stretch now than it was just months ago - if they really feel you deserve it…