I had a chance to have a look at some references and some codes (ASCE-07, IBC 2006, NBC and OBC). A good reference is NEHRP (2000) recommendations which can be downloaded from:
(Chapter 4). The latter is a reference of all the codes that I have reviewed.
As I understand the previous versions of the codes were developed based on the relative impedance between the overlying soil layer and the underlying rock mass. This is why in the previous versions the amplification factor for a site consisting of Rock was considered to be 1. The new versions are developed around the theories presented in Borcherdt (1992, 1994) which consider the average shear wave velocity in the upper 30 m of ground profile. Basically it needs the time required for the shear waves to traverse the upper 30 m of ground. This is why in the new versions of the codes Site class C or D is considered as base and all other seismic factors are calculated based on that, i.e. factors for site class s C or D are 1 and for better sites are less than one and for poorer sites are larger than 1.
Based on the above, following are some thoughts:
1 - the important parameter is the soil condition in the upper 30 m below the foundation. So, if rock happens to fall within this depth it should be considered in the site evaluation.
2 - In all the codes the basic study method is evaluation of the shear wave velocity. Other methods like SPT 'N' Val;use or Su can be used for this evaluation as well. Only Nib's commentary has the comment that shear wave velocities can not be inferred from SPT or Su. If you look at the attached reference (which is a main reference for NBC) page 275 second column 1st paragraph, it clearly says that if shear wave velocities measurements are not available Su or SPT 'N' values can be used to estimate shear wave velocities and get the average over the upper 30 m of soil profile. Further, ASCE-7 has a sentence that in the presence of rock the SPT 'N' value can be assumed to be 100. NEHRP also states that SPT 'N' values should not be considered more than 100. Therefore, I think either estimating shear wave velocities from SPT or Su, or assuming an SPT of 100 for rock and using the equations presented in all the codes for averaging is a rational method in cases that mixed soil conditions are encountered.
3 - When we have piles going to competent bearing layers I think again the important factor is the soil profile in the upper 30 m of soil-rock measured from bottom of the pile. However, special attention should be paid to the effect of liquefiable soil or soft soils on the piles during earthquake. If the surrounding soil loose its shearing capacity the pile will buckle and the whole structure will be in danger. I have seen in some cases people assume that the piles have some improving effect on the soil and depending on the relative stiffness of the piles and the surrounding soil a site class is chosen which is poorer that Rock and better than the original soil condition.
I appreciate your further thoughts and comments.