Scent

[Willtell]

While under a Darkness spell a creature with scent locates the square a pc is in. If the creature attacks does it still suffer a 50% miss chance because the pc is effectly invisibile?.

 

[Dr. Zoom]

It cannot pinpoint the target unless it is within 5 feet of it, according to the DMG, page 81, only its presence. In either case, it would still suffer the 50% miss chance in the same way anyone would suffer the miss chance even if they pinpointed an invisible target with a high spot/listen check. Pinpointing the target means you don't have to guess it location, but the miss chance still applies because scent is not blindsight.