It is a lot. A bulk discount would be nice, but alas, you're paying the same per Atari point no matter how many you buy.
Most C-Store items aren't available in the game. The VA level ships are an exception, but their in-game cost is also prohibitively high (after you get one free). In the end, none of it affects gameplay.
I assume that they would be either transferred to whatever currency that Perfect World uses, stays the same, or there will be two types of currency for awhile with a c-store purchase of buying the new currency.