The rules say:
Aircraft were highly potent weapons for attacking AFVs. If an aircraft scores an X result on the Direct Fire table against a hex containing an open-top AFV, the firing player may choose to target that step loss to the open-top AFV (the player owning the AFV does not get to choose which unit in the hex takes the step loss as is normal (7.61)). If the aircraft scores a 2X or 3X result on the Direct Fire Table versus a hex, he may target one of those step losses to ANY AFV in the hex, not just an open-top AFV.
So if there is an attack on a stack of apc's and an X is rolled one is taken out. If a 2x is rolled 2 are taken out. If a 3x is rolled are 3 taken out? Per the wording above it doesn't sound like it but I'm not sure if that was the intent or not.