Isco is quite likely to get a spot in the NT if he keeps playing like this for Madrid, and with call-ups throughout the year Del Bosque will get a good feel for how to use him.
Illarramendi is a big maybe. VDB might finally see that it's time to kiss Alonso goodbye, but his backup options for that would be to drop the double pivot all together or to use Martinez in that role, which makes it difficult to find a spot for Illarra. He might, depending on how he plays over the season and if he gets any consideration for a spot, but there's more doubt on that.
Thiago seems doubtful at this point. He's still finding his true place at Bayern, he hasn't broken out yet form-wise or looked notably impressive compared to the other Bayern players, and this injury just screws up any chance he has of being able to fully adapt to the team before mid-season. It's possible, but very unlikely at this point, it'll take time for him to get to his best and impress VDB.