The article says "Metrolinx’s contractor will be replacing spans and support beams, repairing masonry, and upgrading the structural capacity of the aging Speed River Bridge", so it sounds like the the piers and abutments are being retained.
The bridge structure is already future-proofed for double-track:
View attachment 319278
But it doesn't sound like this particular work will be installing the structure for the second track. At most the spans that are getting outright replaced might get a double-track span instead.