The way it works is that the client and server pick a "rendezvous node" (the server generates 6 HSDir entries, each with 3 random nodes every day, and the client picks a random HSDir entry and a random one of those node to use). Then, they communicate through the rendezvous node which doesn't know who the client or server are (because both are connected through Tor circuits and neither reveals the .onion URL that was looked up in the HSDir).

The way the statistics work is that some Tor relays opt-in to sharing statistics about how many HSDir lookups happened through them, and then those figures are extrapolated to figure out how many .onion service accesses happen. The relay doesn't know which service is being looked up, and the rendezvous node doesn't know which service is being talked to.