From Coronis:

Have had some confirmation on the Kami Trio. Seems like they aren't mission based but are akin to how the random legends appear in previous series. Landorus is found on 8/F of Breezy Plains, but it's not a guarantee appearance (its name simply appears in the Pokemon that can appear list). I have encountered one but it didn't join me after I killed it.

As for the other two, it seems like we have to depend on the random warp thing of the dungeons. The Golden Chambers are back, and the higher the level of 'mystery' of the dungeon (as denoted by the numbers 1 to 5), the more likely you get warped to these 'map-less' dungeons. While the commoner place is the 'Mapless Street' where you can find the starters and Axew, occasionally you get warped to a Golden Chamber. Thundurus is found in the Golden Chamber accessed via the Iron Rust Mountain, and Tornadus is found in the Golden Chamber via the Large Glacier. Since the level of mystery is reset each time you finish a quest / dungeon, I think the easiest way to encounter these Golden Chambers is when these dungeons have Mystery 5. Again, it's random whether you go to the Mapless Street or the Golden Chamber, and despite their names present on the list, they may or may not appear again.