It would of course depend on what the terms of these contracts are. I would have thought that it's not possible to have conflicting contracts running concurrently i.e. club and super 15, giving each entity exclusive use of the player's (employee's) services.
At the end of the day, like all employees, players have a choice as to what, if any, contracts they sign. If they sign something with a Shute Shield club, giving that club first rights to his services, that club would be able in theory to prevent the player playing tests, super and 3T. Is it seriously suggested that such contracts are in existance? If so, I'd suggest that the players concerned are either happy to play no higher than club rugby or are very poorly advised.
No-one has corrected me on this yet, but as I understand the model, test and super players will not play club rugby at all. They will play super rugby until the tests start, then those selected for the Wallabies will play in the tests and the rest of the super players will play 3T. There's no window for club rugby, except perhaps a player returning from a long injury break. The role of clubs will be reduced under this model to grass roots development and playing Shute Shield, once players reach elite level, the clubs won't see them. I'm not saying it's good or bad, it's just how I understand the new model.