Which allows for faster queries in a graph database: a node with multiple properties, or a node that points to multiple nodes?
With the given information, I find it difficult to give you a simple answer.  As you have discovered, data can be hierarchical with many different logical groupings that could work.

Here is a checklist of things you can do to get a better answer for yourself:


What are the full set of queries you will want to do?  (Among your
schema options, which one(s) minimizes the number of times you're
going to disk to retrieve data for your set of queries?) 
How will your data set scale?  (Among your schema choices which one(s) scale gracefully, minimizing the number of fat nodes or other degenerates
that will not scale well?)
What kind of churn do you expect?  How much are you willing to slow writes in order to accelerate reads?


I hope this helps.