You could put some platform, for instance a UAV or a recon plane, in the area. It will then link the targets for the subs, and they will fire missiles. I guess the subs won't use the missiles if the targets are unknown to them etc.
You can also use the (it's in "doctrine language" or "script", can't remember which) function "enter solution", which works at least for playables. I think you could use that for AI subs as well. If you enter a solution of a hostile cargo ship for an AI sub, I guess it should then attack the target. (Haven't tried, so I'm not sure.)
Usually I don't have this problem, if I make sure the hostiles have some form of radar or ESM intelligence.
Miika
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Constantem Decorat Honor
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