Sure, if by paying 1000 on the wards for grade 5, while you pay 4500 on the vendor, you mean it doesn't make sense. Then sure, your a pioneer of an entire new logic system.
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Well, things are changing anyways, as you can read RIGHT HERE:
1. There will be a “Repair NPC” and a “Merchant NPC” stationed at every Aetheryte/Settlement.
2. When an NPC repairs an item, the level of durability will be restored to 99% of the item’s condition.
3. Only crafters are able to restore an item’s durability to 100% (As per the design)
4. The price for NPC repairs will be greatly lowered.
(The price per item will be fixed at 100G/500G/1000G/2100G/5000G according to the level of the equipment)
5. The cost of Dark Matter will be lowered.
(G1/G2/G3/G4/G5 = 50G/300G/700G/1500G/3500G)
6. The decrease in condition based on equipment deterioration changes are as follows:
No decrease in status/attributes for durability levels between 100 and 1
As Coglin stated, we could still have some profit selling gathered dark matter, but I expect a drop on sales rates if we take above information into consideration.