Saix never trusted Xemnas. Of course not. Xemnas, or rather—Xehanort—ruined his life, but he did think that Xemnas needed him. Which was true, but obviously he didn't know what it was Xemnas actually needed him for. No, he believed that he had made himself invaluable due to his work because they both had the same goal: to complete Kingdom Hearts. He believed it even more when he eventually realised that Xemnas knew he was a traitor and yet continued to pretend that he didn't know.
There was another thing he believed too. Considering that Xemnas was willing to continue their charade—the one of noble superior and loyal subordinate—Saix thought that Xemnas saw him a as a worthy opponent, someone of equal standing to play mind games with. It gave Saix a sense of being in control, a sense of having power.
Of course, this was never true. Xemnas never saw Saix as an equal, just as an easily manipulated tool. Saix was so prideful, so stubborn, so desperate. His attachment to Axel made it even easier to control him and the best thing was that Xemnas could do this without Saix suspecting that he was being strung along.
Most of the time, anyway.
Because there were times when Saix suspected differently. When everything started to unravel, when things seemed to fall apart and go against their plans Xemnas seemed way too calm. Like it didn't matter, as if all they did in the Organization was just a cover for something else, something bigger, something that Saix was not in on.
It didn't help that Xigbar would tease Saix by dangling vague hints of that possiblesomething else over his head only to pull it away before Saix had a chance to grasp it. It unsettled Saix, but he would shrug it all away. If he acknowledged that something else than what he'd believed for so long might be going on then that would mean that everything he had done had been for nothing. It would mean he had never been in control, that he been played for a fool the whole time. It would mean that he'd been wrong and he just couldn't have that, could he?
And so Saix fell right into Xemnas' trap, just as Xemnas had known he would.