Decorrelating Stationary Colored Gaussian Noise -- Effect On The Desired Signal
Yes, the "Whitening" is basically filtering the signal using an LTI System.

The Result would be the signal $ \mathbf{s} $ filtered by the system which whitens the noise.

In the framework of Matched Filter this is OK since you will be able to filter the Reference Signal as well and hence have the same performance.

Yet for other usages you must take under consideration the effect of whitening system.