1.- I usually make a hidden perception roll, unless the palyers state otherwise. Which is the size of the magical mark, or the trap in question? Give them a penalty to the roll if it's hard to spot. Where is it located? Secret rolls are my way to go, but if you don't like it, try to speak to your players and tell them you usually lay traps arround, and whenever they feel something they should be using their skills. D&D 4E threats perception and insight as passive skills, again, a secret GM roll would solve all of this without creating a GM vs player scenario.
2.- Depends on the trap. Is the Sign plain visible? Anyone without magic knowledge would recognize a sign, but that doesn't means they KNOW it's a trap. Let's imagine a Fighter with Knowledge (Arcana) skill, he's not a wizard, but he may KNOW the sign is a trap with a succesful roll. A rogue without mystical knowledge might spot it, but think it's a thieve signal and just pass by it, triggering the trap. It's a trap, it can be spotted, but it takes the players to analyze it and understand it, just as an automatic arrow shooter hidden in the nose of a Moai Statue, or a doll that will shoot needles one you pass by her side. If the sign is being hidden by some spell, then you would need more work and caution to spot it, and that would need the player to actively use a skill, not solved with secret rolls.
3.- Just say it's a symbol. If they decide not to check it, they'll trigger the trap. If they decide to be cautious, they might eb able to learn it's a trap. It's a elarning anyways, if they trigger it, next time belive me they'll think twice before ignoring a signal, and if you made a secret roll and warned them, they most likely won't blame you or call it "unfair".