edmeister,
Not only does the CSK reduce the net area at the hole compared to a protruding head with the same shank diameter, and create a sharp notch, but it also changes the bearing stress profile and distribution based on the csk angle. This can actually get complex when you consider most aircraft holes are not just installed in areas of far-field tension, but due to joint geomety are subject to secondary (eccentric) bending. This also has an effect on the bearing stress dsitbribution. Furthermore, due to variability in installation, using a csk head fastener can also have an effect on the hole filling factor.
You can read about this in:
Schijve, Fatigue of Structures and Materials, Section 18.5
de Rijck, Stress Analysis of Fatigue Cracks in Mechanically Fastened Joints
And yes the stress concentration will change if the fastener is installed. You are dealing with rivets it sounds like, but this is especially true for transition fit or interference fit holes and holes which have been cold worked prior to installation.
There is a difference between the Kt of an open hole and a filled hole.
Useful for this is the concept of the stress severity factor. This is presented in Niu Airframe Structural Design page 238. Like most things with Niu it is basically just a bibliography as he has taken the equations and figures straight from Jarfall.
One thing you will note is that the SF presented there does not account for CSK. In industry this is commonly dealt with using generally OEM data for additional "gamma" factors which can be applied to the SF based on the depth ratio. These range from 1.0 for a straight shank to 2.0 for severe cases of CSK.
If you don't have availability of this, you can try modifying the SF based on Sparweb's suggestion, or you might find this paper useful:
Stress Concentrations for Straight-Shank and Countersunk Holes in Plates Subjected to Tension, Bending,and Pin Loading
Shivakumar and Newman
Another interesting paper which discusses the fatigue life of joints including countersinks is:
NACA TM 1395
Keep em' Flying
//Fight Corrosion!