Honestly, the Emperor was right to deceive me at first. He's right that I wouldn't have trusted him. Case in point: I did not trust Omeluum in my first run when I was actually trying to roleplay and make somewhat genuine decisions (not "it's a game, let's just see what happens" decisions). I didn't even do its quest.
Ideally, someone would be honest with you so that you can decide, with all the info, whether to trust them or not. But desperate times and all that. He needed our trust. The fate of a lot of people depended on it. Even if he only cares about saving himself, it's still saving a lot of other lives too, including ours.
Also, plenty of people hide or change things about themselves for their own safety or comfort. Queerness, disability, religion. Things like makeup, hair dye, clothes, and surgery can change how we look. Many people don't even use their real name or share pictures of themselves online.
Also, half of our companions lie or manipulate or withhold info from us too. Astarion tries to manipulate you by seducing you. Astarion, Shadowheart, Gale, and Wyll all withhold important info about themselves.
Also, what does it even matter? Elf, half-orc, mindflayer, what difference does that make? He was still doing what he said he was---protecting us.
Also, he's pretty honest about everything else. He tells you right away that he stole the power he's using to protect you. Tells you he's doing this because he wants to be free of the Absolute. Tells you he ran the Knights of the Shield. Tells you how he got captured by Gortash, mind controlled again, and sent on the nautiloid to find the prism. And when he tells you the tadpole powers will help in your fight, that is also simply the truth.
I have never felt any sort of betrayal from the Emperor.