That really sucks!! You would think they could just pass the bike through an xray system and be done with it
Depends what facilities the airport has. I flew Philadelphia to Venice in May. The Philly international terminal does not have a scanner large enough to accomodate a bike box, so my box was opened. Venice does have such a machine. I put my bike on the conveyor, it went through the scanner and the woman screener literally gave me a "thumbs up."
One of the people who was on the trip did not fare so well. Somehome managed to crack his hard case and chainstay of his carbon fiber bike. He said it looked like a forklift had been used to move his box since there was a horizontal slit in the side of the box about the size of a forklift blade.
Whatever accessories you put in the box should be firmly affixed to the frame or the side of the box. Personally, I carry my pedals and skewers with me.