Speaking as an EE Undergrad at McGill(in Montreal), I don't think it will affect her at all. I've been using linux exclusively for nearly a decade and in my experience, everything that has worked for other students' (windows & mac) computers has worked for mine. This includes everything you mentioned except classroom applications.
For the most part, any program I've needed for class has run perfectly fine using WINE(well, technically crossover linux that I get when there was a free give-away) except for a program that I needed to program a Lego NXT robot (BricxCC), but even in that case there was a linux alternative that I could have used had I been so motivated.