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In neo4j should all nodes connect to node 0 so that you can create a traversal that spans across all objects? Is that a performance problem when you get to large datasets? If so, how many nodes is too much? Is it ok not to have nodes connect to node 0 if I don’t see a use case for it now, assuming I use indexes for finding specific nodes?
There is no need or requirement to connect everything to the root node. Indexes work great in finding starting points for your traversal. If you have say less then 5000 nodes connected to a starting node (like the root node), then a relationship scan is cheaper than an index lookup.
To judge what is better, you need to know a bit more about the domain.