Not Every Option Is Explicit
The entire point of the ruleset presented in the Dungeons and Dragons roleplaying system is that it does not cover every conceivable circumstance. Wizards create custom spells, strange creatures never heard of before can exist in ancient forgotten forests, feats and classes and powers that are not in the rulebooks should abound. The DM is given the role of gatekeeper for this sort of stuff, as they are supposed to be impartial about content in a way that players aren't.
Any GM who tries to stick strictly to the existing content, and does not allow things like 'using skills in an unlisted way' or new spells or whatever, to the limit of balance and verisimilitude, is missing out on a large portion of the game.
- Permanency has a short list of allowed spells, but adds that the DM can add others. Antimagic Field is an obvious candidate.
- Flux Slime is a natural planar substance that creates an anti-magic field.
- Dead Magic Zones (DMZs) - They occur naturally or 'around the sites of magical cataclysms' (in faerun). They operate as an AMF in most ways, except in faerun (shadow weave magic still works).
- Resetting Traps - A Self-Resetting Antimagic Field Trap is CR 7 and costs 33,000gp, creating a permanent area of antimagic.
- Energy Transformation Field - A ETF keyed to Antimagic Field with an automaton activating an infinite use magic item (such as three *immovable rod*s) inside a space inside the field continuously, casts the spell on a continuous basis every time it goes down.
- Stronghold Builder's Guidebook (updated 3.0 material) has Sigils of Antimagic, which add Antimagic properties to a single 'stronghold space'. It costs 66000gp.
there are more Wizard Tricks that can replicate this sort of thing.
Whether you're allowing expanded, permanent, static antimagic fields as a use of the permanency spell, as magic devices (death star force field generator style), or as a custom spell, it should cost XP to cast.
XP is far superior as a costing mechanism for permanent effects than GP as it is a straightforward measure of power instead of the weird in-between of GP, and there's no real way to arbitrarily get more of it. Without cheesy methods of regaining XP (Thought Bottle, Negative Level/Restoration Dance, Dweomerkeeper) it is a steady, measurable cost for doing business.
Assuming it affects more than just a 10' radius area, 1000 XP is a fair price for a permanent antimagic field. One 10' cube per level per cast seems fair.
Level: Clr 9, Magic 7, Protection 7, Sor/Wiz 7
Components: V, S, M/DF, XP
Casting Time: 10 Minute Ritual
Range: Long (400' + 40'/Level)
Area: One 10' Cube/level
Saving Throw: None
Spell Resistance: See text
An invisible barrier surrounds a space you designate. The space within this barrier is impervious to most magical effects, including spells, spell-like abilities, and supernatural abilities. Likewise, it prevents the functioning of any magic items or spells within its confines.
An antimagic zone suppresses any spell or magical effect used within, brought into, or cast into the area, but does not dispel it. Time spent within an antimagic zone counts against the suppressed spell’s duration.
Summoned creatures of any type and incorporeal undead wink out if they enter an antimagic zone. They reappear in the same spot once the field goes away. Time spent winked out counts normally against the duration of the conjuration that is maintaining the creature. If you cast antimagic zone in an area occupied by a summoned creature that has spell resistance, you must make a caster level check (1d20 + caster level) against the creature’s spell resistance to make it wink out. (The effects of instantaneous conjurations are not affected by an antimagic field because the conjuration itself is no longer in effect, only its result.)
A normal creature can enter the area, as can normal missiles. Furthermore, while a magic sword does not function magically within the area, it is still a sword (and a masterwork sword at that). The spell has no effect on golems and other constructs that are imbued with magic during their creation process and are thereafter self-supporting (unless they have been summoned, in which case they are treated like any other summoned creatures). Elementals, corporeal undead, and outsiders are likewise unaffected unless summoned. These creatures’ spell-like or supernatural abilities, however, may be temporarily nullified by the field. Dispel magic does not remove the field, though Mordenkainen's Disjunction might.
Two or more antimagic fields/zones sharing any of the same space have no effect on each other. Certain spells, such as wall of force, prismatic sphere, and prismatic wall, remain unaffected by antimagic zone (see the individual spell descriptions). Artifacts and deities are unaffected by mortal magic such as this.
Should a creature be larger than the area enclosed by the barrier, any part of it that lies outside the barrier is unaffected by the field.
Arcane Material Component: A pinch of powdered iron or iron filings.
XP Cost: 1000 XP.
How is this justified?
Magic is assumed to be, in many ways, a Field. A localized, saturated energy that can be called upon to perform magical effects, power magical devices, and empower magical creatures.
Without that magical field (such as in the area of an antimagic field or a dead magic zone), spells do not work, dragons cannot breathe flame, magical items do not function.
The Antimagic Field spell specifically destroys all magical energy inside it's radius of effect. A permanent version of that spell is an effect that does that on a permanent basis.
That's the in-game justification of that. A magical effect that in some way removes all magical energy from an area (by blocking it off, or using it up, or whatever).
There is no standardized system for costs and requirements for custom spells and effects
The DM has to set that. Rule of thumb, eyeballing, comparative analysis, dark powers of Chaos, call it what you will, the basic mechanical art of encounter design looking at things and evaluating them for mechanical balance, and is a key skill for any GM. Applying that to spells is a simple matter of reading through similar effects and estimating what you need to do to create a spell, feat, ability, magic item, or naturally occurring (Na) effect to mechanically iterate the effect or ability you are trying to create in the world.