I am not an expert but my personal opinion is malfunction, a well maintained modern submarine has a lifespan of about 30 years and thats without any damage as a result of combat. The Dakar was a WW2 design submarine, it had seen combat during the war and was over 20 years old at the time it was sold to Israel. So this thing should have really been retired already. When they found the Dakar there was no evidence that the crew were expecting to going so it is unlikely to have gone down as a result of combat. It could have been hit by a Soviet sub by accident but if another sub was going to be close enough to accidentally ram they would have detected it on sonar before they got within ramming range but there was no evidence they were expecting it. what matters now is that there are no more tragedies. What I don't understand is why some of the documents are still classified considering the incident happened so long ago and Dakar wasn't even on an operation at the time it was sailing from the UK - Israel.
We want Iran cooperation, not meddling, Gulf Arabs tell Kerry (Reuters)
from the article: How did Israel's Dakar submarine sink 45 years ago?