Material costs being significantly lower than shard costs are a result of a new game with many people leveling gathering classes. Anyone trying to level up those classes can only mine shards until about level 5, after that the exp is just too low, so instead they're farming up the same ore or log for 5 levels. This means that right now are a side effect of leveling the gathering class while most of the shards are directly mined as a source of income.

Materials are temporarily low and (without RMT assistance) will inevitably rise as the game gets older and everyone their brother aren't leveling up their gathering classes. It's not that shards are way too expensive, but that materials are way too cheap right now.