In the rules it states that when a Pokémon evolves it becomes free of Poison, Sleep, Confusion, Paralysis, or anything else that may be the result of an attack. Does this mean that damage is also taken off of it when it evolves?
If an opponent already has Nidoking's Toxic double Poison, then next turn I use a "normal Poison" attack, does the opponent retain Toxic's double Poison condition or does it now become a single Poison condition?
It would gain a single Poison effect (the new effect replaces the old one).
Dark Dragonite's Pokémon Power does not have the "you cannot use this Power if your bench is already full" text like most other Bench-building powers and attacks do. Does this mean that by using Dark Dragonite you can bypass the normal five-Pokémon limit to your bench?
C'mon. That's silly. There isn't room to put the reminder text on every single card. The rule is the bench can only have 5 max (EVER).
Dark Pokémon evolve from Basic Pokémon. Once you evolve a Basic Pokémon into a Dark Stage 1 Pokémon, it CANNOT evolve into a non-Dark Stage 2 Pokémon, only a Dark Stage 2. "Once you walk down the Dark Path, forever will it dominate your destiny" - Yoda the non-Pokémon.
Some players freely examine their own discard pile (or their opponent's) whenever they want. Is this allowed? Or can a discard pile only be examined when you have official business there (like after playing Item Finder).
Discard piles are open knowledge (either player could look through them).