I'm seconding John (Battlezone)'s thoughts here as i've put in 12mhz versions into both Asteroids and Missile Command and measured them and the crystal isn't putting out an exact 12mhz anyway, it gives out 12.03 and then as it heats, it settles to around 11.95.
I was curious about this when I repaired a couple of boards so measured it on my scope.
From an engineering point of view, as the games speed and everything else is derived after the crystal via various dividers, the aim was to generate 6mhz, 3mhz and 1.5mhz in most cases. A lot of the circuitry and game code is tied to the vertical sync which runs at 59.97khz and can't fluctuate by a vast amount anyway so the original use of 12.096mhz is likely more "what they had on stock" than anything else.