Ballot papers that are protected by the Canada Elections Act would still be protected by the Access to Information Act insofar as the personal identifiers are concerned.
Under the proposal that came from the House to the Senate, technically it would be possible for an individual to request access to the ballots, as happened in Florida in the dangling chad case. The Senate decided it did not want that level of openness to exist with respect to ballot papers. I'm not sure of the rationale, because if someone wants to pay 20ยข a page for every ballot paper to have access to them, then be my guest. But it would not infringe upon the confidentiality required to run an election.