These same objections could be raised about the concept of 'generic supplies' as well. How do the quartermasters know exactly how much fuel, food, ammunition, etc. to load all the time? That's why many games -- like the MOO series -- use a fixed radius of operation to simulate the supply train, and some others -- like SE III -- use a fixed number of turns.
The use of explicit supplies is a good thing. It lets you have ships with greater or lesser range at the same technology level and allows greater endurance for less activity rather than forcing you into one fixed range or one fixed time limit. I like having supplies explicitly included in the game, and I hope crew quarters and life support will honor their 'supplies used' settings in SE V!
I also think the concept of 'generic ordnance' is a good one. It splits off the biggest 'exception' to the supplies problem -- the difference between combat usage and regular usage -- and makes ship supply consumption a bit more logical at minimal cost in micromanagement. The additional bonus of being able to give heavier weapons a disadvantage of running out of ammunition is also good.
There are many 'issues' like this in simulation games where full realism is too difficult or burdensome to adhere to. I for one can live with the 'problem' of apparently interchangeable ammunition just like I can live with the 'problem' of interchangeable supplies because it enhances the game.