Number 1, as has been explained, is that Adria spent the interim 20 years between D2 and D3 marking the souls of the Lords of Hell. As for why Diablo and Mephisto weren't destroyed when their soulstones were shattered, there's no real concrete answer. It's very possible, given the mysterious nature of the original soulstones and the Black Soulstone, that they will be discussed in greater detail in some future book or an expansion. In the meantime, all I can offer you is some theories:
1) Evil cannot be destroyed. Much like Diablo's death at the hand of Imperius in Wrath, the Great Evils always return because they are more than just beings; they are the embodiment of their Evil. So long as Terror exists, so will Diablo, so long as Hatred exists, so will Mephisto, etc. Considering how often this has occurred, it is a plausible explanation.
2) The nature of the soulstones is unknown. Tyrael believed that destroying the soulstones would destroy the Evils, but he simply lacked knowledge on the nature of soulstones. Considering the Black Soulstone is even more mysterious than the original soulstones, this is also a possibility.
3) Destroying the soulstones was necessary because they were corrupted. Seeing as how the soulstones were shards of the Worldstone, and seeing how Baal corrupted the Worldstone and then Tyrael shattered it, it's possible destroying the soulstones was meant to ensure that the Evils had no anchor to the mortal realm, requiring them to regenerate at the standard rate. Adria, however, got to them first.
As for number 2, they allied with the Nephalem because it was the right decision to make given their desperation and because Tyrael vouched for them. However, not all angels agreed with this decision: Imperius and his host stormed out of Heaven due to the Nephalem interfering. In fact, the only angels that straight out accepted the Nephalem were the angels that voted to spare them in the first place: Itherael, Auriel, and Tyrael.
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1) Evil cannot be destroyed. Much like Diablo's death at the hand of Imperius in Wrath, the Great Evils always return because they are more than just beings; they are the embodiment of their Evil. So long as Terror exists, so will Diablo, so long as Hatred exists, so will Mephisto, etc. Considering how often this has occurred, it is a plausible explanation.
2) The nature of the soulstones is unknown. Tyrael believed that destroying the soulstones would destroy the Evils, but he simply lacked knowledge on the nature of soulstones. Considering the Black Soulstone is even more mysterious than the original soulstones, this is also a possibility.
3) Destroying the soulstones was necessary because they were corrupted. Seeing as how the soulstones were shards of the Worldstone, and seeing how Baal corrupted the Worldstone and then Tyrael shattered it, it's possible destroying the soulstones was meant to ensure that the Evils had no anchor to the mortal realm, requiring them to regenerate at the standard rate. Adria, however, got to them first.
As for number 2, they allied with the Nephalem because it was the right decision to make given their desperation and because Tyrael vouched for them. However, not all angels agreed with this decision: Imperius and his host stormed out of Heaven due to the Nephalem interfering. In fact, the only angels that straight out accepted the Nephalem were the angels that voted to spare them in the first place: Itherael, Auriel, and Tyrael.