Its my impression that subs at sea do not use "active" sonar except when manuvering in tight spots and then in "burst". They use "passive" or listening sonal and other devices at all other times. Using active sonar advertises their position to a potential enemy.
This is correct.
Let's walk through this using the information given. USS Philadelphia doing traning mission with SEALS near FL Keys. Now, the advantage of a submarine is undetectability. Most SEAL missions are covert. Neither the submarine nor the SEAL team(s) are very interested in turning on spotlights and dye markers and other attention-getting devices to advertise their position. This would, in time of conflict, be an open invitation that says "Here we are, please blow us all to Hades..." Since a training mission will be a simulation of actual wartime conditions, you can rest assured that the USS Philadelphia was NOT using (here's the operative word) ACTIVE sonar during this exercise. They were most assuredly using sonar however. The inactive variety. Like sticking a microphone in the water and listening...
Now there's a thought. All those dolphins beached themselves because they weren't informed that it was kareoke night and they all got mike-fright and ran towards shore....