Sub v sub was not so rare. Both submerged, yes, I understand that was rare, actually, I didn't know of any examples until this thread. But in the Pacific a large number of surfaced Japanese subs were sunk by US subs, including one boat that sank three Japanese subs on a single patrol (Batfish). As far as I know, only one known example of a US sub lost to Japanese sub. I recall in Silent Victory the comment that ironically this US boat was lost to the sub it was sent to intercept.
Batfish's 6th war patrol
http://www.ussbatfish.com/patrol-6.html