Say a shotgun has 8/40 shells. I assume the first level of suit ammunition would make it 8/48. The extended mags makes it 12/36, which is the same starting ammo count. Does the suit ammo make it 12/44 (+8) or 12/48 (+12)?
If you are talking about carrying additional magazines as a suit upgrade the suit takes into account the default ammo for the weapon and not extended magazines (since extended mags is an upgrade and not default to the weapon). I believe that is what you are asking yes?