Hi Vishal,
When dealing with square waves as inputs to oscilloscopes there are a couple things to lookout for. The first thing is that the bandwidth of the scope should be 5-10x greater than the frequency of the square wave. This is because the component frequencies of the square wave edges can be much much higher than the the fundamental frequency of the square wave. If your bandwidht isn't great enough, you will see a distorted/rounded almost sinusoidal square wave.
The second thing is that the termination inside the oscilloscope will make a difference as to how the square wave appears. If you use a high impendence termination 10k ohm (1M ohm) you will get the correct amplitude for your square wave but there might be reflections that will distort your
waveform. If you use the 50 ohm termination, this will more closely match the impedence of the wires and will result in a much cleaner square wave but the amplitude of the square wave will be roughly half of what it should be.
As for your last question, the minimum frequency of the 653x boards is 1 Sample/10minues. So I'm not sure why it is not working for you. I have tried using the example Continuous Pattern Output.vi that ships with LabVIEW and I connected the least significant bit to a E Series counter and it measured the 0.5Hz signal correctly. It could be something with the programming of the card. Anyway, hope that helps. Have a good day.
Ron