The best thing I have seen on S-boat operations is the predictably named _Die deutschen Schnellboote im zweiten Weltkrieg_ by Gerhard Huemmelchen (Verlag E.S. Mittler & Son, 1996). It covers S-boat operations in every theatre and every year. It has 257 pages and 24 pages of photographs. Alas, it's out of print. AIUI, Harald Fock's _Die deutschen Schnelleboote 1914-1945_, which is in print, is a pretty standard work, but it may be more of a design history than an 's-boats in action' type of book.
In English, Tarrant's _Last Year of the Kriegsmarine_ has some info on S-boat ops in 1944-1945. ISTR reading a decent enough book on S-boat ops in relation to D-Day some years back. Looking at the illo of Tent's _E-boat Alert_ on Amazon, either it was something else, or else the Airlife edition had a different cover from the USNI one.
Out of the first page of results on Google for 'schnellboote 1939',
http://www.wlb-stuttgart.de/seekrieg/km/sboot/sfl-
frames.htm looks be the most interesting in that it has lists of ships sunk by S-boats and S-boats lost.
HTH,