Your vote is still secret - the serial number exists solely to protect the integrity of the vote.
Countering ballot box stuffing
The serial numbers on ballot papers enable strict accounting of all ballot papers issued and cast. That way, the number of papers found in the ballot box at the end of the election can be tallied with the number issued during the poll and the number of ballot papers stocked before the polls opened.
If a voter casts a vote pretending to be someone else, numbered ballot papers will allow the court to match the suspicious ballot paper with the counterfoil, on which the voter's registration number is recorded. If any suspicious activity is proven, the vote will not count.
How is my vote still secret then?
Theoretically, it is possible for anyone with access to the ballot papers to identify who cast a particular vote. Matching the numbers between the ballot paper, counterfoil, and electoral register can reveal a voter’s identity
However, ballot papers can be examined only under strict conditions, and there are safeguards that make it extremely difficult to find out how any particular voter voted.
All ballot papers and their counterfoils have to be sealed in the Supreme Court vault for 6 months, after which they will be destroyed.
During those 6 months, these documents can only be retrieved by court order. The court will issue such an order only if it is satisfied that a vote has been fraudulently cast and the result of the election may be affected as a result.
I am working on Polling Day. Do I still have to vote?
Polling Day Do's and Don'ts