I really dislike HW, so I don't miss it not being part of the main series. However, I'm still a little confused as to why it's not there. Four Swords is there and that was originally just a bonus game for the ALTTP gba remake. It's always felt like an oddity to me.
I don't think it's going to happen. Even though I personally think HW has a very interesting story behind it. I would love to see it become a part of the official timeline but that's never ever going to happen. To be honest ity would be very confusing because where would they even put it? But it has become my fav zelda game to play (yes even as a spinoff).
Its already totally canon, everone in botw is wearing blue scarves... the trend caught on after HW Linm saved hyrule, everyone in btw started wearing them, like how in Wind Waker young kids get tunics to wear for their birthdays.
Cia used the gate of souls to travel to time and recruit the villains of that specific time. Because of this, the characters were able to exist all at the same time. After the events were over, Lana returned them back to their own time. The thing that would be a bit more tough is the Zant situation. Because he was already dead after Midna got her true form back. And Cia turned Midna back into an Imp in HW. Unless of course, Cia revived Zant soon after this. But then Zant wouldn't have struggled againt her I guess.