I came across many players who are members of NTs but dont have a club team anymore. What happened to their previous club teams? Are those players going to disappear or we can still try to transfer them in the next window?

Good question, I have the same thing.

Their previous clubs were cut due to league size rearrangement.

Not exactly, two of mine are created players whose managers switched teams so they were removed from the team. They are still in the NT, though.

It's possible his former manager left the club (if they are created players), or the club was closed due to the rearrangement of the league size.

Those players without a manager can't get selected in the next national selection (right now for example) I suppose. I don't think they are available for transfer either unfortunately...

It's discussed a bit in the bug forum before by the way :) :
http://rockingsoccer.com/en/soccer/forum/bugs?topic=848