Was I supposed to perform the Blackroot ritual three times?
I did the Blackroot ritual once, where Rhalic teaches me how to use Spirit Vision. Then I got my second Source Point from Hannag, at which point the Narrator suggested that I should perform the ritual again - but I did not do it. Instead, I went ahead and got my third Source Point.
Then the Narrator once again suggested to perform the ritual one last time. Almost as if implying that I already did the ritual twice.
So now with three Source Points, I performed the ritual - technically my second time doing it. Rhalic taught me Source Vampirism, and then told me to go the Nameless Isle. Siva was killed by two Voidwoken.
Did I miss something from the fact that I didn't perform the ritual three times? It seems to me like the game expected me to do it three times, but when I try to perform it a third time, the Blackroot fumes have no effect on me so I can't visit Rhalic again.
Did I miss some extra dialogue or perhaps a third skill? (I imagine Vampirism is the second skill)
Hannag mentioned that she could suck the Source out of living beings so it made sense to me that I got Vampirism as second skill. The third Source point I got was from Mordus, who said he could control the minds of others, leading me to believe that perhaps I should've obtained a third skill similar to possession or something.
Solution 1:
You don't miss any powers by performing it only twice instead of three times. (In fact, it's possible to perform the ritual only one time, granting both powers at once.)
After one Source point, performing the ritual grants you Spirit Vision.
After two Source points, as you suspected, performing the ritual grants you Source Vampirism.
After three Source points, performing the ritual will simply grant some dialogue with your god. Upon your return, you'll find Meistr Siva dead.
This video shows the intended progression: