Unfortunately...
...that aspect of the AI (i.e. HQ decision making) was overlooked or simply kept to the basics. I guess it depends on how realistic you want to play the game. In real life, ignoring your orders would have extremely serious consequences when you got back (assuming you got back) however in the game you are free to pretty much do what you want. You can spend months and months simply popping into Midway or other locations for refuel/resupply and patrolling anywhere you want without returning to your home base if you so desire. There is no major penalty for doing so.
It would have been a nice touch to have much more variety in the responses to radio calls back to base. I don't know if it's a moddable aspect of the game. IOW if you let base know you've expended all ammo prior to your end of mission they should respond with "RTB to nearest resupply point and continue with mission orders" or "acknowledge, RTB for resupply and new patrol orders". You can obviously do that in-game but it's not really reflected in any radio traffic.
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