I really don't buy the "ammo stored everywhere" being the problem with the conversion of expendable ammo to new ammo relics. Ammo essentially being a consumable reagent, and consumable reagents having already been "removed" from the game without any trouble (Hey there, Blinding Powder!).

Also, there's precedent for old-for-new trading quests (Old epic mounts for the new ones), so it's not a huge stretch to consider that it's possible to "replace" old ammunition and allow players to trade them for the new relics.

The process goes like this:
1) Rather than replace existing ammo types with equivalent ammo relics, just add the relics as new items. Not hard, since this is something Blizzard has done with every patch.
2) Then replace the existing ammo types with equivilent junk/quest items (Like how Blinding Powder became Worthless Blinding Powder), stackable to their current size (For instance, if Terrorshaft Arrows become Dulled Terrorshaft Arrows, Dulled Terrorshaft Arrows still stack in lots of 1,000). Again, this is not hard, since Blizzard already has done this in recent history.
3) Now set a price for the new relics and then sell them at ammo merchants in place of the original ammo types. Increase the cost somewhat. If a player then wants to just replace their ammo with the new relic, they can just buy them straight off the nearest ammunition dealer. Not hard.
4) Create a few quests to allow players to trade old ammo for new relics. I'd wager that most Hunters, if they weren't low on ammo before the patch, tend to try and keep above 5,000 rounds of ammo, so use this value as a trade price: 5,000 dulled ammo for 1 ammo relic. Make the quest a one-time only trade (So anyone who stocked up on ammo beforehand can't make a killing just trading ammo for expensive relics), and not count towards achievements such as Loremaster and Seeker. Give these quests to, say, Bounty Hunter Korlak in Orgrimmar and whatever his Alliance counterpart is. Y'know, the guy that trades Thorium Shells for Thorium Headed Arrows. Since Blizzard already has done quests like this, this step shouldn't be hard.
5) If you want to drive the point home for players who don't read the patch notes, and to stall any questions of "omg my weapon dun work", send out an in-game mail to all Hunters (And maybe Warriors and Rogues) from Korlak (Or his Alliance counterpart) telling them that they're interested in trading antique arrows and shells for new gear. Blizzard has done this with the riding skill changes, so this isn't hard.

All it takes is some effort.

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