All depends. If you sub was damaged before the save, upon reload, the sub is returned back to the damaged state and this includes the 'we are taking damage' and the noises associated with the damage.
If you were not damaged, I'm not sure. It is always best to save away from other ships and also save will on the surface. Although SH4 saves are not as buggy as SH3 is, it still does screw up sometimes.
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“You're painfully alive in a drugged and dying culture.”
― Richard Yates, Revolutionary Road
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