Wow ! Yamaha seems to have had problem with the gearbox the last ten years on their 4-strokers ! I remember my dad had problems on his YZ426F back in 2001 !
I thought Yamaha had taken care of those problems by now !
No one I know has personally broken one. In fact, I have never broken a gearbox in any bike, including some that actually were weaker than they should have been. I use the clutch, but not always. What I don't do is shift under a lot of power, or make high speed downshifts without either the clutch or a blip of throttle to unload things. My son, who I taught to ride, and who thrashes his bike as hard as anyone, hasn't had one fail either.
The big YZF trans was originally imported from the YZ250, and was used with minor ratio and pitch changes through 2002. The first generation 450's got a 4 speed with wider gears and beefed up shafts. People nevertheless managed to break them occasionally. When the Gen2 engine came out in '06, the 450 got a new 5 speed that is 12mm wider overall than the Gen1 was, but still people figure out how to break them. People break everything else, too.
IMO, it's more the rider than the bike. Yamaha could make the trans indestructible, but there would be a weight penalty.