In the manual, they suggest avoiding the enemies and collecting the divers. That is one possible strategy, but between the fact it nets you fewer points and the fact it takes longer for divers to appear, I suggest shooting first and asking questions later.
Another tip: When the interference sub starts appearing, it's best to resurface with your crew at the far left side of the screen if the interference sub isn't onscreen. That way, if it does appear, you'll have more time to avoid it. If you're about to resurface when the interference sub is already onscreen, I suggest pulling up behind it and resurfacing.