Version 0.2 of the Basic rules includes a list of Forgotten Realms deities, and it looks like most of the old deities have returned, including some that died before 3e was even released. Bhaal, Leira, and Mrykul -the three you mention in your question- are all back on the list. So are Azuth, Mystra, and Savras, and most of the other popular formerly-dead deities. However, there are a few entities who haven't been mentioned yet that one might have expected to see, such as Xvim and Asmodeus.
Nonhuman pantheons are not part of the "big" list, though they do get a brief mention in that section. The Dwarven pantheon, at least, appears to all be back: all the old names are listed, but stats aren't given. The same likely holds for other races. Animal deities, like Nobanion and Lurue, also aren't listed.
In any event, the Basic rules don't give any history or other reasons for why this happened. The PHB and DMG might explain further, or this could be relegated to the novels.