Considering that stacks are essentially ways to interpret raw shot quantities, anyways, I don't get your objection there precisely.
Just because you can wing it easily doesn't mean it's actually inferior to display it as a raw number. I've heard people say that the raw numbers game can be misleading in Roguelikes and that you should go with your gut-and there's some validity to that, I feel-but that's taking it to a rather rough extreme. Stacks represent X shots and you're just doing rough mental math really fast(Or kneejerking based on past experience that you have enough shots...same difference.) to get the actual values-you can just as easily gutcheck a totaled value the same way.
The real reason I can see to support this, though, is that I'm constantly having to go into my inventory for no more reason than to check my ammo. Why should I? That's like having to Shift+2 to see my HP. It's a vital statistic. Even if some clarity is lost-which I very much disagree that any is-it's worth it for the convenience value.
Personally, I think just displaying the ammo remaining on your primary weapon would fix the clutter issues. It's not quite as Doom-like but it strikes a nice compromise between HUD clutter(DoomRL has to display more info than Doom, after all) and useful, relevant information.
Oh, and "You shouldn't be having ammo problems anyways" is a better argument for removing ammo than lowering the amount of information given. After all, you shouldn't be having ammo problems anyways, therefore it's not a useful statistic. (I do not agree with this, either, naturally.)