The point is spending those coins will slow down the client right now b/c it takes forever to collect enough 0.00000001 LTC to make up a large enough value to send. So I changed the create transaction code to ignore these tiny values by default to speed things up. If you really want to spend them and wait forever for the client to create the transaction, you can by passing in a tiny min input.
You could also ignore these transactions (under the min amount) when checking blocks for wallet transactions. It will help improve the general performance of the wallet going forward too.