BART does not currently run 24/7 primarily because they have to perform maintenance on the system, some of which requires that trains are not running. This is especially the case for the Transbay Tube which requires a lot of attention.

If BART had two tubes then they could run 24/7 and still complete the required maintenance with shut down periods staggered at different times for each tube. This would allow the full system to remain running 24/7.

I've heard it stated that one reason BART doesn't run 24/7 is that they regularly need to be able to shut down a track to do maintenance. More track provides redundancy that allows them to redirect traffic from one track to the other when doing maintenance on it.

There is more information about this on Quora: http://www.quora.com/Why-does-BART-need-to-do-nightly-mainte...

I can't speak to BART, but in Vancouver when people ask why our trains don't run 24/7 the answer is always "because we need maintenance windows". Maybe the second transbay tube would allow them to keep one tube open while they do work on the other tube?

Track maintenance.

Having dual track throughout the system, and tube redundancy, allows track work to occur without delays and/or danger to track crews.