It’s set to 9:41 because when the iPhone was first announced to the world, Steve Jobs wanted the time displayed to match the exact time it was in the room.
The first ever iPhone was unveiled on January 9, 2007, at the Macworld Conference & Expo held in Moscone West in San Francisco, California… More here.
It’s a similar story for traditional watches, but the reason is much more obvious. Using the time above is more symmetrical, it highlights all of the markers and it has become so familiar that an analogue watch looks weird when advertised with a different time shown.