AFAIK it all starts from importing a blockchain into a graph database..
What exactly is a graph database? Making things visual is just so we as a human can easier understand things. At a lower level it just tables and columns
What will be the impact of this analysis with the rise of LN, sidechains and other anonymity solutions?
Anything no longer recorded on-chain (like with lightning) isn't available on the blockchain so it can't be used for analyzing.