If you go by the common interpretation of "munitions" and by and large the contents of that list, then it clearly does was not intended to include mathematics.
I think you are trying very hard to imagine inconsistencies where there are none. Not only are you trying to argue that cryptographical software is not relevant to military uses, which is an absurd argument to make, but you are also trying to argue that managing what items feature in an export control list is not the responsibility of an executive branch.
The only requirement to export-control something is that the item features in an export-control list. You're complaining that a specific type of software was added to such a list. Tell me exactly what part you don't, can't, or refuse to understand.
That's a rather facetious interpretation. You're complaining that there was no law preventing software being distributed, and as there was a need to prevent that then lawmakers fixed that problem. That's hardly surprising, isn't it?
You also seem surprised that including cryptography software in existing lists designed to prevent export of military and/or dual-use technology is also surprising, unexpected, or outlandish. If you actually think about it, is it really?