Yeah there will be more updates although you will probably have to wait for Chinese national day to settle down and EZManager to get an update first (it need ones far more than EZClient currently does), there is also an update of EZ4 Client to come.
The GBA compability of EZ-Flash II is near to perfect.
Even Pokemon series works fine, because EZ-Flash II has RTC (Real Time Clock) feature.
If you´re not talking about NDS compatibility, there´s no need to update EZ Client/EZ Manager.