I'm sure you're thinking that Indigo is involved with Kobo, so there's no reason for them to go in a different direction. But Indigo also sold off their interest in Kobo a while ago, so now Kobo is only a partner like WH Smith, Whitcoulls, or Pearson Australia. (Indigo is probably also tied to Kobo by contract, so this post is likely irrelevant. But that won't stop me.)
Now, Kobo is said to be the dominant ebookstore in Canada, so one might assume that Indigo would want to stick with it. But have you considered how Kobo got that position? It's not through looks or personality, but because Indigo was the largest Canadian bookstore chain. In store support adds a lot of value; just ask B&N. But it would add value to any device supported by Indigo, not just Kobo.
So if Indigo formed a partnership with B&N, there would be value in it for B&N, right? That seems like a good reason for B&N to try to recruit Indigo, if you ask me. At the very least, it puts Indigo in position to negotiate a better deal with Rakuten - assuming B&N is interested, of course.
What's more, B&N is already selling ebooks in Canada, so expanding to have a real presence up north would make sense.
On the other hand, I could see B&N expanding into Canada without Indigo as a partner. I'm sure that it would be nice to have a bookstore, yes, but B&N is already absent from a good chunk of the US anyways. And several of B&N's current US retail partners also own chains in Canada, so negotiating new agreements wouldn't be that difficult. Tech support also wouldn't be that much of problem; it would have to be online and phone but B&N already does that. The only major change would be the legally mandated support for French, but that is a minor issue.
In any case, I foresee Canada being B&N's next market. They might even announce it at the same time as the Waterstone's deal.
image by brewbooks