Well, I think that would involve editing the weapon_equip.ini file and selecting which guns require ammunition. Example:

[Munition
nickname = br_gun02_mark03_ammo
hp_type = hp_gun
requires_ammo = false
hit_pts = 2
hull_damage = 158.100006
energy_damage = 0
weapon_type = W_Particle01
one_shot_sound = fire_particle3
munition_hit_effect = br_particle_03_impact
const_effect = br_particle_03_proj
lifetime = 1
force_gun_ori = false
mass = 1
volume = 0.000100

[Gun
nickname = br_gun02_mark03
ids_name = 263392
ids_info = 264392
DA_archetype = equipment\models\weapons\br_railgun.cmp
material_library = equipment\models\br_equip.mat
HP_child = HPConnect
hit_pts = 1923
explosion_resistance = 1.000000
debris_type = debris_normal
parent_impulse = 20
child_impulse = 80
volume = 0.000000
mass = 10
hp_gun_type = hp_gun_special_6
damage_per_fire = 0
power_usage = 39.520000
refire_delay = 0.187500
muzzle_velocity = 1350
use_animation = Sc_fire
toughness = 6.300000
flash_particle_name = br_particle_03_flash
flash_radius = 15
light_anim = l_gun01_flash
projectile_archetype = br_gun02_mark03_ammo
separation_explosion = sever_debris
auto_turret = false
turn_rate = 90
lootable = true
LODranges = 0, 20, 60, 100

"I would have the ammo take up cargo space, but its not really what im looking for
im talking about a ship that can have 5000 ammo for a weapon (like bullets) and extra maximum ammo for missiles depending on the missile attachment (Heavy missiles have one, low yield dumb-fire rockets are around 16).
Then again, my idea for afterburner feul as ordinace may have to be scrapped if this dosent work, as it thrives on being able to increase max ammo for a script beyond the typical max for a ship (usually standard at 180 and +50 for each pod)"

Well, if you are going to make bullest where you can hold thousands to be realistic, there is no other way than to make missiles, mines, cms etc. take up cargo space. Because the ammo limit apllies for all that, and 5000 missiles is just unrealistic and ridiculous.