Jeff,
1. The nudging is applied every time step, which is 30 minutes in WACCM. Where did you got the idea that it is every 6 hours? The wind and temperature fields are nudged at every time step toward the analysis fields by 10% (default), or whatever fraction you set in the namelist variable met_max_rlx. The output is the model predictive field after nudging, which will be different from the analysis field unless you set the nudging to 100% (met_max_rlx=1.0)
2. The "standard" version of WACCM is neither SD nor SC; it calculates both dynamics and chemistry interactively. SD (specified dynamics) was developed to reproduce specific winds and temperatures, mostly for studying how well the model calculates chemistry in comparison to observations. SC (specified chemistry) was developed for users who are less interested in chemistry, and want to study how well the model calculates dynamics. The advantage of specifying chemistry using output from a previous WACCM run is that the model will run about 2 times faster. If you are more interested in studying dynamics and care less about chemistry, SC may be the configuration you would want. If you do care about interactive chemistry, you can use a standard free-running configuration of WACCM with full chemistry for double the cost of SC. SD is the most expensive version of WACCM because the number of vertical levels is increased from 66 to 88, and the model must calculate all of the dynamics and chemistry done in the standard version before nudging the dynamics.
I hope this helps.
Mike