[3.5] Leomund's (Phantom) Trap

[Venger]

Would you then similarly not get trap sense bonuses against a Shadow Conjuration version of Create Trap since it's not in fact a trap? Honest question; I don't know how this interaction would work

That's not the same thing. A shadow conjured trap is still a trap and functions as a trap. the only thing you successfully disbelieving will do is make you take a fraction less damage from its arrows or what have you.

A silent image of a trap that you failed your save against, for example, is not a trap, so even if you thought it was, you would not be able to get a bonus against it.

Rules bonuses are based on objective reality, not your perceptions. Like I said in the other example, if you're a ranger and have favored enemy (animal) and run into a druid in wild shape, your favored enemy bonus will not apply to him since his type didn't change.