Well, he did say the truth about getting paid by Atari, and gave him "his half", which Woz regarded as "good enough compensation", otherwise he wouldn't have considered working with him in the future. It's kind of the same game played when a middle manager that brings no value to the company gets paid 3x the engineers salary, or when the CEO gets the golden parachute while the shareholders are loosing money and the employees are getting salary cuts or the company is getting downsized... but you don't go around calling people "liars" for playing this game as the corporate level, do you? Yeah, it's no longer "lying" because the information is theoretically available to all players, or at least to the IRS, but it's kind of the same game.
Woz probably didn't became upset about it because by the time he found out about that little incident, he was in some kind of "managing" position himself, and "playing the same game" but in his advantage now, and he was there because of the other decisions that Jobs made, so...
Basically what at the small "garage business" is called "being a liar" is what at the bigger levels is called "the rules of the game". And yes, you're no longer a "liar" and no longer breaking the rules, but simply because the rules are bent the way you need them to be bent.
The only alternative would be to have only fully transparent employee owned companies... and we all know this is not how our current flavor of capitalism works :)
EDIT - TL;DR: it's basically the same "bad" deal one gets in any employee employer relationship, just that they didn't have this explicit relationship