If you want to use national security as a justification for subsidies, you need to be careful with what you are subsidizing. Only essential things should be subsidized. Non-essential things can be left to the market, or at least their subsidies require other justifications.
From a national security perspective, it is essential to provide basic nutrition to people when international trade is disrupted. Having access to food people enjoy eating is not essential. The viability of existing agricultural businesses is not essential. The preservation of cultural traditions related to food and agriculture is not essential. And so on.
It's also important to consider where the subsidies should be directed. Here in Finland, the explicit justification for agricultural subsidies has always been the assumption that food produced in "European countries that still have a strong farming industry" might not be available during a crisis.
From a national security perspective, it is essential to provide basic nutrition to people when international trade is disrupted. Having access to food people enjoy eating is not essential. The viability of existing agricultural businesses is not essential. The preservation of cultural traditions related to food and agriculture is not essential. And so on.
It's also important to consider where the subsidies should be directed. Here in Finland, the explicit justification for agricultural subsidies has always been the assumption that food produced in "European countries that still have a strong farming industry" might not be available during a crisis.