I literally just spent hours researching/testing this in game because I have noticed some funky things when it comes to total ammo I can hold. All I can really say is pay attention to the numbers for each gun and armor that gives you more capacity for it.
What did I learn?
1 Running upgraded mag on my machine gun "The Swarm" is a good thing. (72 default mag/no perk, 109 default mag/with perk, 168 mag upgrade/no perk, 181 mag upgrade/with perk.)
2 Running upgraded mag on my fusion rifle "Final Rest II" is a bad thing. (27 default clip/no perk, 34 default clip/with perk, 25 clip upgrade/no perk, 31 clip upgrade/with perk.)
3 I get one less bullet for my shotgun "Invective" when using Queen's Gaurd Robes instead of Voidfang Vestments.
4 "3" is not true for my shotgun "The Comedian."
5 The ammo increase is different for apparently every single weapon.
6 I have no idea how Bungie came up with values for ammo capacity (most of them are not full clips or even nice ratios unless the clip is really small.)
7 You can't copy pasta from excel neatly into these GUI's (sorry for the format, I tried I promise.)
8 One can't really use "stacking" to describe using more than one ammo perk for the same gun, because it's not strict addition, (using boots and chest piece for my bad juju the bonuses are about 23% each and 46% together, for my rare pulse rifle the bonuses are 20.97% each, but together only 36.83%.)
Class Gun Type Name Ammo Bonus Clip / Mag Size Total Ammo Capacity Total/Clip Ratio
Exotic Hand Cannon The Last Word 0 8 78 9.75
Exotic Hand Cannon The Last Word Chest 8 97 12.125
Rare 20 Hand Cannon Renegade MK. 55 0 5 82 16.4
Rare 20 Hand Cannon Renegade MK. 55 Chest 5 97 19.4
Exotic Pulse Rifle Bad Juju 0 15 273 18.2
Exotic Pulse Rifle Bad Juju Leg 15 336 22.4
Exotic Pulse Rifle Bad Juju Chest 15 336 22.4
Exotic Pulse Rifle Bad Juju Leg + Chest 15 399 26.6
Rare 20 Pulse Rifle Primed Starfall MSC 0 27 391 14.48148148
Rare 20 Pulse Rifle Primed Starfall MSC Leg 27 473 17.51851852
Rare 20 Pulse Rifle Primed Starfall MSC Chest 27 473 17.51851852
Rare 20 Pulse Rifle Primed Starfall MSC Leg + Chest 27 535 19.81481481
Legendary Fusion Rifle Final Rest II 0 6 27 4.5
Legendary Fusion Rifle Final Rest II Chest 6 34 5.666666667
Legendary Fusion Rifle Final Rest II 0 8 25 3.125
Legendary Fusion Rifle Final Rest II Chest 8 31 3.875
Exotic Shotgun Invectice 0 4 15 3.75
Exotic Shotgun Invectice Chest (Queen's Guard) 4 19 4.75
Exotic Shotgun Invectice Chest (Voidfang) 4 20 5
Legendary Shotgun The Comedian 0 5 22 4.4
Legendary Shotgun The Comedian Chest 5 26 5.2
Legendary Rocket Launcher Admonisher III 0 1 5 5
Legendary Rocket Launcher Admonisher III Chest 1 7 7
Exotic Machine Gun Super Good Advice 0 58 139 2.396551724
Exotic Machine Gun Super Good Advice Chest 58 200 3.448275862
Legendary Machine Gun The Swarm 0 35 72 2.057142857
Legendary Machine Gun The Swarm Chest 35 109 3.114285714
Legendary Machine Gun The Swarm 0 60 168 2.8
Legendary Machine Gun The Swarm Chest 60 181 3.016666667
Again sorry for the format, this looks much better in the editing window.
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Holy mother of god.