Is it possible to query the Clickhouse db directly from another application, e.g. Mode Analytics or a Python script?

Yes. But it depends how you have deployed it. I have a default SigNoz docker deployment for playing with and I can connect to the remote Clickhouse DB (using DataGrip). I'm not sure if the QueryService API will provide the data that you need, but that should probably be your first port of call. That way you're not building a dependency directly on the underlying database.