No, it's still in effect. If you look at any time schedule, some regions of it are printed with a gray background. Those are the times bikes are not allowed on BART. But the gray areas vary by station. I work in the East Bay, and on my way home in the evening, no station east of SF is ever gray, but the SF stations starting with Embarcadero are. This means that at rush hour, I can take my bike over the Bay to Embarc, but there I would have to get off. Which I don't do btw... but I work at off hours, so it's rarely a problem for me anyway.
I actually like BART a lot, the only problem is that the trains are not frequent enough and they don't have a fine enough network of lines -- I'm spoiled by what I grew up with in Europe. I also look forward for the more bike friendly cars. It's also not really cheap (I pay $6 for a round trip each day!), but it's still plenty cheap in comparison to operating a car.