Why am I hard pressed to find framing nails that meet code at my local retailers?
You say, "For example, the IRC calls for 16d common nails (3-1/2" length, 0.162" shank) all over its fastening schedules."  This is true, but it also lists (in same schedule) how many 3" x 0.131" nails or staples are required. (See IBC Table 2304.9.1) 

For instance, Item 16: Stud to Bottom Plate: 2 - 16d; or 3 - 3" x 0.131" nail; or 3 - 14 gage staples. 

I don't think the Building Officials are ignoring the nailing requirements for various fasteners.  I think they know the required nailing for pneumatic nails or staples.