Hi Arnero,
If you use DAQmx, you can expect excellent performance for a driver library. DAQmx Read or Write performance when using a single digital port is less than 20 microseconds using Windows a Dell 1.6 GHz computer. On LabVIEW RT, using an 8176 controller, I have benchmarked the performance to be less than 5 microseconds per read or write. Make sure you start the DAQmx task outside your inner loop to get best performance.
A 1KHz loop rate should be no problem. However, if you are using Windows, you can occasionally expect the system or other applications to interrupt your program. This interruption could cause a significant delay. If you use a real-time OS like LabVIEW RT you can get expect better determism and less jitter.
If you need register-level programming, you can use the "Measurements DDK". However, your application will be easier to write if you use DAQmx. Your loop rate is fairly slow, so I would expect DAQmx to work just fine and you shouldn't need to do register level programming.
Jonathan