You're not actually trading coins directly between wallets on a coin exchange, once your deposit is credited to your account the balance exists as a database entry and is incremented/decremented based upon trading, deposits and withdrawals. Essentially your coins become virtual so the decimal point rules of the client itself become irrelevant at that point. An exchange could add as many decimal points as they want but most stick with 8 because that's the standard set by Bitcoin.

The only time the 2 decimal point limitation would be an issue would be at the time you come to withdraw as the client won't allow you to send transactions with more than 2 decimal points anything in the remaining 6 decimal spaces would be dust that you can't withdraw.