My only suggestions would be to first look at the seller's history and other items. Are they selling a lot of loose copies of this game or other loose but brand new looking GBA cartridges? Then it's very likely not an official release. Loose carts that look like they've got some wear on them (they are over a decade old at this point) are more likely to be legit.
Secondly look for copies with the original boxes, this will cost more but I doubt many pirates have bothered replicating the boxes and manuals. Ultimately it may be cheaper to buy Aria of Sorrow and Harmony of Dissonance separately since I think the double pack release was rarer. It might also be easier to find legitimate copies of Circle of the Moon since it was a big seller and a launch title for the GBA, it's also a great game and beats the pants off Harmony of Dissonance imo. Just make sure you're playing with a backlit screen when you play Circle of the Moon, which means playing it on the GBA SP, DS, DS Lite or Gamecube Game Boy player. But those are really the best way to go to play any GBA game anyway.
If you do wind up with a fake copy, the main thing to worry about is the battery, you'll want to replace it with a (if I recall right) standard cr2032 watch battery which you should be able to find in a lot of stores.