So I received a dated schema that used to work well at the beginning but it's experiencing some scaling issues.
Among of them, the space used by the indexes is catching my attention so I would like to know if they are being used, how many times, etc.
Other that explaining/profiling queries, is there anything else I could use to have this kind of information?
The information you are looking for would be under metrics monitoring, but index accesses is not one of the available metrics Neo4j provides. (Neo4j supports Prometheus, but I don't know if Prometheus captures that info either)
But there are some indirect ways you can get this data.
Assuming you have a test server that replicates production, with appropriate load tests, you can try removing the index and seeing how it affects the load tests. (This way is a bit cumbersome, but probably gives the most accurate measure of how varies DB changes affect performance, but only if the load tests accurately reflect production use.)
Alternatively, for a more static analysis, you should only be executing pre-defined, parameterized cyphers. So you can Profile/Explain those Cyphers against the DB at different scales, and compare those notes to the Cypher logs (either calling end, or using Neo4j metrics monitoring) to get an idea of how often each one is called.