Hey BB1,
For these “21 Tournaments over 21 Days” with card counting turned “on” then shuffling will happen at the end of the hand. If not then shuffling will happen when the deck is half way through.
For all other regular tournaments the Card Counting feature is one that is set by the tournament director when the tournament is created. So some will have it and other not, however a player can see beforehand what the exact ‘rules’ are for a tournament… see the example screen shot below:
Hope this helps 
Shane