A couple ideas:
An artificer could easily become a magic item salesmen that can get by with a small ammount of markup (and occaisionally reselling an item 'as-is' for a solid profit). Having the ability to disenchant without the ritual cost, and with a simple feat, being able to make items quite far above their own level.
Part of the reward system suggested is to provide the players with a certain ammount of cash, or cash equivalent treasure, in addition to magic items. The magic items you receive are above your level, and more expensive than most items you could purchase (and would be impossible to actually 'make' with a ritual without special tricks like the feats from the Eberon Player's Guide).
To say that you can't spend this cash of magic items ... greatly limits the value of the money. While potions and other consumable magic items, and rituals, have their uses, eliminating the option of purchasing magic items makes the money packages much less useful. One solution is to convert a portion of that cash into extra magic items. You could easily take the value of a level+1 item out of the cash treasure packages, and still have enough left over for consumable magic items and the like.
As for restricting purchases:
Magic shops could very easily be a situation of "mother may I", in which the players request an item they are looking for, and see if they can find a way to purchase it. It could easily be a way of hiding the "get DM approval" step behind an in game excuse of "you can't always find everything you are looking for", and makes sure that not only can the DM disallow items they disapprove of, but can also ensure the DM has some idea of what each of the players can do, and perhaps also confirm questionable ideas immediately (for example, if a player has a question of how an item interacts with a feat and a power, for example, they can address it while trying to purchase the item, and may even decide against it at the same time.)
The Enchant Item ritual provides another problem in terms of in game justification for certain items not existing. One issue is that, unlike with buying a magic item, you need to get access to the ritual components. Rarely will the PCs have all of their cash packages come in the form of ritual components, so they would still need to go to town to convert the cash into components. Just as you may not be able to buy anything you want, there could be a limited ammount of ritual components available for purchase. You can also disenchant, but that requires destroying existing magic items, so it would be trading down (or trading in a lot to get one good one). While banning items would require a justification, it doesn't require an in game justification to simply limit the ammount of ritual components the PCs have at any given time.
This would effectively create three tiers of magic items. Items above the players level they find, and are entirely DM's Choice. Items near their level are too expensive for them to get the ritual component's to make, so they have to buy them from a store, and thus, are subject to DM Veto. Finally, relatively low level items, and consumables, are cheap enough that the PCs with the correct ritual can just make it himself, in which case it's just about anything goes.
In all cases, the purchase or creation of the item should at least be acknowledged by the DM.