Prices are computed to the nearest penny for electronic transactions (credit/debit cards, for example). Cash transactions are rounded up or down to the nearest $.05.
My first time spending money in Canada was in 2007, and I did have Canadian pennies in my change. Fast forward to 2015, when I next visited Canada, and suddenly the penny was no good. They did accept the pennies at a welcome station where I was converting them, along with nickels and dimes, to quarters.