It has a zero timeout, not zero timebank (80 days timebank) so it wont be bothering you for some time yet! IMO though I think that taking timeouts in tournaments, whatever the time constraints, is fair enough. Tournaments (and clan matches) have that extra level of competitiveness that means that anything is fair game.
Personally I wait for the automatic timeout to happen. It's 2 days, which is probably less grace than I would give an opponent anyway, and if it's the system that took the timeout no-one can POSSIBLY get upset with me.
Remember though the problems that happened in the 2005 Championship because neither player was taking the timeout. The automatic timeout was triggering because they weren't taking 48 hours to make a move but they were still out of time and thereby extending the game beyond the intended max of 120 days.