The suburban (and LU) platforms already had canopies - they were altered over the last few years to match the straightened platform edge, (eg P5?) and the lengthening for longer trains and the area around the new lifts at the London end.
The current DLR and new LO platforms were completely new - so I'd expect TfL specified canopies for the new build.
The long distance platforms on the other hand had no existing canopies (apart from over the stairwells) to extend or alter, so I doubt it was an oversight - there was nothing there to extend or alter so maybe it was just outside the scope of the project.