That doesn't excuse designers from reducing frustration wherever and whenever possible. In general, puzzles are designed to slow you down, to make the experience last longer. They're one of the only ways a designer can control the pace of the game. We've come to expect them, and we'd feel cheated if they weren't a little annoying. It is, however, a small leap to an unwarranted conclusion.
Designers add puzzles which are difficult simply to be difficult.
Never mind advancing the plot. Never mind creating puzzles which flow naturally out of the game's setting. A perfect example of needlessly annoying puzzles. Invariably the hint books sidestep giving a real solution and instead suggest writing a computer program to solve puzzles like this. There are borderline cases, cases in which the annoying puzzles fit well, or at least adequately, in the story.