Frustratingly, the data for this is scant. The AEC only seems to report data in depth when specifically requested to by the standing committee on electoral matters. And aside from reporting on non-voting in 2007, it does not appear that this has occurred.
I will therefore start with 2007, and limit my answer to non-voting, rather than non-registration.
2007 federal election
AEC produced a report to JSCEM on non-voting and multiple voting at 2007 federal election, with detailed discussion.
The key figures are provided in Table 1 on page 7:
Number of non-voter notices sent: 453,600
Number of non-voter notices incorrectly sent due to processing or procedural error: 18,400
Number who provided a valid and sufficient reason for failing to vote: 186,400
Number who claimed to have voted (but claim unsubstantiated): 19,600
Number of warning letters issued: 5,350
Number of non-voter notices returned undelivered: 47,700
Number of non-voter non responses: 117,000
Number who paid the $20 penalty: 59,000
Number of prosecutions resulting from failure to pay the $20 penalty: 64
It therefore seems that of the non-voters with no good reason, and who did not pay the fine (being 453,600 − 18,400 − 186,400 − 59,000 = 189,800), there were 64 prosecutions, meaning the prosecution rate is around 0.03% of non-voters.
2010 federal election
I could not find any data at all for 2010 on the number of prosecutions for non-voting.
2013 federal election
The AEC's annual report for 2014–15 provides a brief mention on page 35:
In late August and early September 2014, summonses were issued against more than 3000 apparent non‑voters at the 2013 federal election. This number was one of the highest on record. Most of these cases proceeded to court and most non‑voters were fined and convictions recorded.
Accordingly to a Parliamentary Briefing, 14,712,799 were enrolled to vote, and the turnout was ~93.5%, so around 956,000 people failed to vote. It is unclear how many of those had valid reasons and how many paid the $20 fine.
The AEC's report on the conduct of the 2016 federal election provides a mention on letters sent for non-voting on page 7:
The AEC identifies apparent non-voters through an examination of the scanned certified lists. Following this, letters were sent to 965,378 apparent non-voters in the week commencing 19 September 2016. If no response was received to this letter, a follow-up letter was sent in the week commencing 31 October 2016. If there was still no response, a final reminder letter
was sent in the week commencing 8 December 2016.
After this process, if the AEC determines that there is no valid and sufficient reason for not voting, the person in question is required to pay an administrative penalty of $20. In cases where neither a response to the notice or payment was received by the due date, the matter may be referred to the courts. In these cases the individual is liable to pay a maximum fine of $180 (plus court costs), and a criminal conviction may be recorded. The court process in these cases is managed by the AEC in cooperation with the CDDP. The AEC is scheduled to commence non-voter prosecutions by mid-April 2017.
I could not find further data on the prosecutions, though given it was relatively recent, that is not surprising.