I agree with Platypus that you had to have done something to give your position away at ~8000 yards and anything over 2 knots on silent is risky. However, I have observed that the stock AI in SH4 is a bit...fruity. I have seen the omniscient moments you have spoken of (mainly in avoiding torpedoes) while also seeing destroyers act dumber than Lumpy from Happy Tree Friends. Without more details of your approach, it will be hard to say what went wrong.
The game does take thermoclines into account, but not in a realistic fashion. If I remember the older posts that address this, the game simulates thermoclines by altering the range of the sonar on each destroyer.
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