Find me a 50-ish-mile distance in the US that is easier to cover by public transit than SF/San Jose. Boston/Providence? DC/Baltimore? Philadelphia/Wilmington? New York/Trenton? Comparable at best, but in all cases, you're generally talking the absolute far edge of regional rail that runs hourly at best.
Peak LIRR trains take less than 90 minutes, with at least one express train in each direction less than 70. There are 13 peak (arrive 6-10AM) week day westbound trains and 14 eastbound (arrive 5-9PM). The longest gap between trains during the week is westbound between 1:46AM and 4:06AM, eastbound it's 1:21AM to 3:14AM. Otherwise rarely is the gap more than an hour.
Ref: http://mta.info/lirr/Timetable/Branch/RonkonkomaBranch.pdf
I am pretty sure that if Caltrain went about 10 miles/hr faster, 101 will have fewer cars.
This is vastly, vastly better service than Caltrain SF-SJ.
It would be nice to have a train leave SF later than midnite, but having taken that train many times, the ridership level is probably break even in terms of costs, at best.
BARTs night time gap at the terminus of most lines is, I think, roughly midnight to 4am, so its not all that different.
> I'm not sure if the Bay Area has comparable density to the DC-Philly-NY-Boston corridor
Not even close. The East Coast corridor you name is the most densely populated region of its size in the US, by a wide margin.
If BART ran those kinds of distances 24/7, it would at least significantly increase the consistently-reachable zone. There's currently some all-nighter bus service, but it's not a great replacement (slow, nobody knows the routes, etc.).