1. Back in the War of the Ancients, some force of kaldorei rebels penetrated the walls of the Palace of Azshara. When the area sunk, they couldn't get out. When Azshara was asked by the Old God if she wants to live, she said yes, and the Old God made every kaldorei naga, for he couldn't care to ask every single one of them if they join him. These rebels have been leading small guerilla operations against Azshara, which is why she has not attacked yet (I mean seriously, what was she doing for 10k years) but now with her getting Neptulon's power, they're beginning to lose, so they ask help from their long lost brothers and sisters, the night elves. The night elves accept them because they prove they were rebels from the War of the Ancients. Also, they didn't come to surface for so long since they were shamed that from beautiful kaldorei (remember, during WotA night elves, all of them, put a price on beauty) they were turned to fish people and they thought it was a punishment from Elune for not having found the evil in their society earlier, so they stood there in shame.
2. Since the War of the Ancients, several generations of naga were born and grew. The younglings don't feel so indebted to the Old God, they don't like Azshara as much, so one day they try to find out about the kaldorei of old and join them to liberate their society from under the tyrannic leader of Azshara and her Old God leader.
3. A tribe of naga felt more and more like they're treated like dirt by Azshara for being lower caste, so they decided to go their own way, and what better way then to join her enemies?
etc, there's so many ideas.
As for armor, they can already preety much wear pants as a sort of skirt, and boots just you can't see them or they're tail rings. What's the difference from draenei or trolls who also don't wear shoes or have special models for them? And every race has a different model to pants. This is not an issue.
As for mounts, how hard can it be to understand, SIDE-SADDLE! There were even pictures showing it, I'll see if I can find one, hold on: