I realize this question is getting long in the tooth (getting old) so my answer is intended for other users who stumble across this question.
From my real world experience, instrumented binaries do run significantly slower, often by orders of magnitude. However, I have only instrumented MANAGED binaries and the OP specifically stated unmanaged C++ so "your mileage may vary."
My suggestion would be to run a subset of the tests that take between 2-3 minutes. Run that subset 3 times and average the actual run time results. Then instrument the binaries and run the same tests 3 times and compute the average. Fewer tests and the data might be skewed because of application initialization. More tests and you MAY end up waiting an hour for each instrumented test.