Firstly, we must underline that the Commitee have esplicitly removed the base shear scaling requirement for dynamic analysis when they have released the 2004 revision of the code. So it's not something merely missing, they actually decided to remove it. I believe the reason for it is to not constrain the designer to stick to an approximate formula that in many instances can be overly conservative. However, engineering judjement must always be used, and we cannot arbitrarly reduce earthquake load as much as we want by simply reducing the model stiffness. Models are too dependent on modificaiton factors (as well as other parameters such as releases or restraints) that are arbitrarly assigned.
So in my opinion the best approaches are two:
1) Stick to the scaling factor of 70 or 80% of base shear calculated from the approximate period formula;
2) Build a model with no releases and no modification factors or releases, run a dynamic RS analysis and use that as a minimum base shear to be used when subsequently changing the structure and introducing releases and modifiction factors.
The second approach is, in my opinion, the more accurate and the one reflecting the spirit of the code better. No scaling to a minimum shear based on an empirical approximate formula, but also engineering judgement tells us that we should not reduce the load simply based on arbitrary stiffness redution factors.
There is a third way of course, which would be to perform a full cracking assessment on every element of the structure and find the real cracked stiffness of the structure, however this would be quite complex and time consuming and I doubt any engineering company would adopt this for any standard project.