Explanations are spoiler-tagged to reduce visual clutter.

SMG Magazine
Steel Bar x1, Iron x1
Small amounts of the most common material in the recipe, as this ammo is relatively weak
Depleted Fuel SMG Magazine
Steel Bar x1, Depleted Fuel x1, Phosphorus x1
Would've also given it iron, but I felt phosphor was more appropriate for the overall cost
HMG Magazine
Steel Bar x1, Magnesium x1, Titanium-Aluminum Alloy x1
One of the rare instances where an ingredient doesn't have an alternative! Included nothing else so as to not make it too good
Assault Rifle Magazine
Steel Bar x1, Magnesium x1, Steel Bar x1, Copper x1
Like the HMG mag, magnesium doesn't have alts. The others are the two most common mats, added for extra padding

Coilgun Ammunition Box (& Coilgun Blanks)
Aluminum x1, Iron x2
Some recipes return ingredients of ingredients - and for that, iron was the perfect candidate, as it's very common and only makes up a third of the ammo's recipe
Piercing Coilgun Ammunition Box
Aluminum x1, Steel Bar x1
Also makes up only a third of the recipe, and is the most common of the possible materials by a large margin
Coilgun Harpoon Box
Aluminum x1, Organic Fiber x1
More common than steel; straightforward enough

Chaingun Ammunition Box
Aluminum x1, Copper x2
Like the normal coilgun ammo, except that chaingun ammo is more expensive and deserves the next most common material
Shredder Chaingun Ammunition Box
Aluminum x1, Steel Bar x2
Like the piercing coilgun ammo, is the most common of the possible materials
Physicorium Chaingun Ammunition Box
Aluminum x1, Physicorium Bar x1, Steel Bar x1
Mostly for a little extra padding, as the less expensive coilgun equivalent normally returns the same amount which doesn't make much sense

Spreader Flak Shells Box
Aluminum x1, Copper x1, Phosphorus x1
To avoid redundancy with the basic coilgun and chaingun ammos; phosphorus is also the more common of the two explosive powders
Focused Flak Shells Box
Aluminum x1, Steel Bar x1, Phosphorus x1
Slightly less common materials from more expensive ammo
Explosive Flak Shells Box
Aluminum x1, C-4 Block x1 Sodium x2, Plastic x1
I don't like removing things, but I felt this would make sense considering that the coilgun equivalent returns sodium instead of C-4 or UEX. Also gives you one of the plastic from the C-4
Physicorium Flak Shells Box
Aluminum x1, Physicorium Bar x1, Magnesium x1
Like the chaingun equivalent, all that's needed is a little extra padding

Unchanged

• Explosive Coilgun Ammunition Box
  
• Depleted Fuel Coilgun Ammunition Box
  
• Physicorium Coilgun Ammunition Box
  
• Pulse Laser Fuel Box
  
• Pulse Tri-Laser Fuel Box
  
• Gravity Flak Shells Box

Ammo boxes must be above these conditions when they're deconstructed, or they will only produce aluminum.
For most, this threshold is ≥90%, changed from either 95 (in every case where a munition mat was already given) or nothing at all, to create a parallel with the ≤10% refill threshold.
However, there are some exceptions:
Coilgun Ammunition Box (& Coilgun Blanks)
∅ → ≥90% + ≥45%
Applies to the iron; this is a concept taken from Gravity Flak, the only vanilla ammo to have two munition mat thresholds
Coilgun Harpoon Box
∅ → ≥65%
For parity with other boxes; gives you a single free shot
Chaingun Ammunition Box
∅ → ≥90% + ≥45%
Applies to the copper
Shredder Chaingun Ammunition Box
∅ → ≥90% + ≥45%
Applies to the steel bars
Explosive Flak Shells Box
≥95% → ≥90% + ≥45%
Applies to the sodium
Gravity Flak Shells Box
≥95% + ≥50% → ≥90% + ≥45%
Applies to the Dementonite