That's very true.
Deus Ex appears non linear, but as you say... it isn't really. It gives multiple solutions to problems and a lot of open ended ways to do things.
I liked the mission in the Versalife building. The MJ12 bit. You could either run and gun, or you could use stealth augs and cloak yourself, hush your footsteps and run past everyone. It was great to have the choice of how to do things.
It also helped being given so much info and story line about what was going on in the game, as it gave you a chance to form your own opinions on what was going on and how you wanted to deal with it.
But yeah, it's not truly non-linear. Just free enough to give a sufficient feeling of free choice.