After reading some discussions about the preservation of ItemIds, I went to some data sites and confirmed that the vast majority of glyphs are either preserved or converted into new glyphs.
I would expect recipes to convert their outputs, glyphs in inventory/bank/AH to convert, and learned glyphs to convert as well.
Here are the glyph conversions for Mage... Note, these conversions may change before 5.0 goes live, but the intention to preserve (most of the) existing items is clear:
Prime
Arcane Blast -> Arcane Power (major)
Living Bomb -> Fire Blast (major)
Fireball -> Combustion (major)
Frostfire -> Frostfire Bolt (major)
Cone of Cold -> Icy Veins (major)
Ice Lance -> Ice Lance (major)
Deep Freeze -> Water Elemental (major)
Arcane Barrage -> Illusion (minor)
Arcane Missiles -> Loose Mana (minor)
Molten Armor -> Crittermorph (minor)
Pyroblast -> Momentum (minor)
Frostbolt -> Faded Glyph (removed)
Major
Invisibility -> Invisibility
Arcane Power -> Arcane Explosion
Mage Armor -> Mana Gem
Polymorph -> Polymorph
Slow -> Slow
Mana Shield -> Counterspell
Evocation -> Evocation
Blink -> Blink
Dragon's Breath -> Spellsteal
Blast Wave -> Remove Curse
Frost Armor -> Armors
Ice Barrier -> Deep Freeze
Ice Block -> Ice Block
Icy Veins -> Cone of Cold
Frost Nova -> Frost Nova
Minor
Arcane Brilliance -> Porcupine
Mirror Image -> Mirror Image
Conjuring -> Conjure Familiar
Armors -> Rapid Teleportation
Slow Fall -> Arcane Language
Penguin -> Penguin
Monkey -> Monkey
Based on this information, I plan to continue prime glyph research daily until the patch.