Gluing the subfloor to the joists when nailing or screwing it down can help a lot with this. What you see is one reason why they require TWO layers of ply for natural stone installations. The edge of a board will act like a lever when there's deflection between the joists. That's also why you don't line up the joints on sheets - the top layer should be 1/4-span past a joist. This can also happen if the subfloor is not installed perpendicular to the joists, as it is much stronger across the joists due to the face grain. If your joist spacing is within specs, you'll probably be okay. Ditra can help if the subfloor is within specs. This is one reason a lot of pros like to install a second layer of ply regardless of whether it is for ceramic or stone. INdustry standards call for a minimum of 5/8" ply on 16"oc joists, but again, most people don't like the minimum, as it leaves little margin for error.
As long as there's no vertical displacement on the cracks, you should be okay.
Precutting sort of depends. Any little miscalculation can be exagerated when setting. On a small room, probably not a big deal - it can be huge on a large install. Off by 1/32" over a row of 32 tile, is an inch, which would likely be unacceptable. But, if you have layout lines and are constantly correcting as you go, it's not as big a deal. Depends on how many, if any, critical things you have in the middle. If it is a clear, unobstructed job, since you need a gap at the edges, being off a little isn't a big issue as long as the baseboard will cover it.