I think it's some sort of sound loop problem (as jimbuna said before).
This problem comes with stock SH3 and happened to me several times.
Most of the time it occured when I was submerged, then surfacing again and heard those ambient underwater sounds though I was on surface with diesels on!
Solution: Save game and exit SH3, optionally reboot system and then load your old savegame. It worked for me, but it's an annoying bug from stock SH3.
By the way, I think it has nothing to do with with too much traffic going on. It happened to me occasionally, even when there was no ship around!
Happy hunting!