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 
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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.https://en.wikipedia.org/wiki/Graph_database
In order to perform an analysis you must have the right tools. Actually it's not just tables and columns if you compare graph to relational databases. They have been designed for different scopes.