But if you can just plug the "pistol ammo" which is available in thousands of rounds into a machine gun (just because bullets have the same diameter) and wipe the entire level empty, then... well then you've done something wrong.
Logistics would disagree. Actually if you could design a round and set of weapons platforms that let you use the same ammo in your side arm as in your squad support weapon and have them all be effective in combat, then you would have a holy grail of weapons development on your hands.
However when it comes to 'end of the world' kind of things, then the question becomes 'how wide spread are these rounds, the weapons, and spare parts for them?'
Do you keep that 5.8-caseless pistol on your hip, because you can use the same ammo for it as you're feeding into your squads 5.8-caseless assault rifles and the fully automatic light machine gun, which everyone loves because of how effective the round is while also saving 15% of the weight on ammo, or do you pick up the 9mm pistol and a few magazines of ammo for it because you hardly ever actually come across any of that amazing 5.8-caseless ammo?
So you've run out of ammo for your 5.56 assault rifle, and now you've fallen back to just your pistol. You come across a 7.62 assault rifle and a cache of ammo for it:
Obviously you're probably going to want to grab that 7.62 rifle. Even if is a little harder to aim and you can't carry as much ammo for it at a time, it is still clearly a far better weapon than your empty 5.56. The question is, do you keep that nice 5.56 in the hope of coming across another cache of ammo for it, or do you ditch it and its dead weight so you can grab another few handfuls of 7.62 ammo to feed the new rifle awhile longer?
But honestly if you want solid answers to these design questions then I suggest that you start writing out stories of what your players actually do. Picture two friends talking about the game, one has played it and one hasn't: What aspects is the player telling his friend about? What awesome and amazing things happened in your game that the player is going to tell his friend about that the friend is going to be interested in.
I've never once said "Oh man, the DPS between weapons is so balanced, and they have the perfect number of ammo types!" when trying to get someone interested in a game. Yes, weapon balance is important, but it is something secondary to the actual game and mechanics itself. Like I said before, I've played games where I had the choice between dozens of weapons, and I've had fun. And I've played games where I've had only a single weapon and I've still had fun. However the number of weapons has never been something that stands out in my mind.