Take a look at the outcome of the fleet maneuvers of the last years

A conventional "SSK" 209 boat "sank" the flattop of a carrier group several times, and a 206 type did that with a 688 - "virtually" of course, but undetected. The 212 is a development, that can remain under water for six weeks - enough for almost all scenarios, but a nuclear strike.
I know there are new methods of detection apart from magnetism and anomalies, one of the institutes developing some of those methods for detecting patterns of all kinds is in Goettingen. From slightest salinity changes to changes of surface water ripples, to the russian method of using underwater optical reflection. The thermal backwater of an SSN is another thing and cannot be cured easily.
Apart from those methods the pumps and operation sounds of a nuclear "SSN" can be heard for miles, in blue water conditions, especially from older boats - remember despite rafting and other silencing techniques most of those boats are now 40 years old.
http://www.abendblatt.de/politik/aus...nd-machte.html