Dude if you publish a book no one's going to care about academic discussions about what level of canon it is.
If you want to get pedantic about it, then sure, Star Trek handles the novels by establishing they're a lower level of canon than TV series. Star Wars integrates everything absolutely. And so far Bioware have also taken the line that if they publish tie-in fiction, it's canon. They dealt with that in Dragon Age by establishing a canon timeline and series of events, and in Mass Effect by scrupulously avoiding references to Shepard's gender, physical appearance or love interest.
So, if Bioware follows precedent then yes, the novels will be canon, and the burden will be on them to make it clear it's not, which would be confusing from a marketing perspective ("hey kids, buy this book about Shepard that totally isn't about the real version of Shepard, and nothing that happens in it is what really happened in the official version of the story!").
But honestly that'd be true even if Bioware didn't have that background. It'll be true even to people buying the book who have no idea how Bioware have handled tie-in fiction in the past.
You make a book with a specific version of Shepard - that's the version people will start claiming is the "real" one.
And like, sure, fine, most people play white, male, heterosexual, paragon Shepard. But like, why does that mean that we need books about that too? Sure most players are straight, white, heterosexual, paragon Shepard. But you can be a straight, white dude in a gabillion other games. Mass Effect is one of the very few games where you can choose to be something else.
Asking for novels specifically about that version of Shepard, is pretty much asking to make Shepard a straight, white guy too. But, he already is for you, and that is 100% fine. It's absolutely fine - I like to play a version of Shepard that reflects some of my basic attributes too. But...it doesn't need to be made true for everyone else also.