In this way, the late Jurassic bird skeletons, which have been named Archaeopteryx, were fossilized.
Can I replace the bold part by "which are named Archaeopteryx?
I think that this is a fact. Therefore, we can use simple present.
You can. It changes the nuance of the sentence. The original highlights the fact that this name was given to them at a later point - but in this case, common sense will tell you that.