Obviously, none of the Lunar cults like the Red Goddess or the Seven Mothers will be around in the Second Age, since they were founded in the Third.
Also, as the Godlearners established their Middle Sea Empire they found lots of different people worshipping gods that were extremely similar, but might have different names, slightly different myths and a few differences in their power. The Godlearners decided that these people were all "really" worshipping the same god, and went round telling people so.
In other words, the cults listed in something like Gods of Glorantha would be familiar to someone living at the end of the Second Age. Earlier on, there would be a lot more local variation - each tribe would worship its own local version of the gods.