Hello dmf,
I am by no means an expert on pro-audio equipment, but I can tell you about the PXI-4461. First off for a description of pseudo differential inputs you can look at this KnolwedgeBase article: What Is a Pseudodifferential Input?
As my understanding of balanced inputs goes, these signals consist of two signal wires and a ground reference. The signals lines carry the same signals, but one line is inverted (180 degree phase shift). This is useful because at any point you can re-invert one of the signals and combine them so that any noise you picked up as a balanced signal is now canceled out. In general this is used to reduce noise caused by traveling through cabling. I believe that most audio devices that support balanced inputs convert these balanced inputs into unbalanced signals early on in an input stage--it is rather rare that an audio device does any amplification/filtering etc. on a fully differential signal.
Since many of National Instruments devices are intended to serve a wide variety of needs we do not specify in terms of balanced or unbalanced inputs since those are industry specific terms. However, when compared to this definition, the inputs on the PXI-4461 are unbalanced in that there are only two wires for each input, + and - (or + and reference if you use pseudo differential). That being said, I believe that most audio stores have boxes that you can buy that convert balanced to unbalanced signals or vice versa. If you want to use balanced signals to avoid cabling noise in your hardware setup then all you'd need to do is get one of these boxes to use for input and output with your PXI-4461.
This is a rather general comparison focusing on the topics that you've brought up. It may be helpful if you can re-phrase your question to ask about a particular capability of the PXI-4461 rather than a straight comparison. As far as the input signal type I don't see much of a difference between the two (assuming you get a balanced to unbalanced converter if you want to use balanced inputs--these are relatively inexpensive). As mentioned in the PXI-4461 Specification sheet, the input and output ranges are +/- 10 V and the rates are 204.1 kS/s. If you need more specifications like that I would suggest looking at that pdf, but if you'd like to describe your application a little more it may be easier to provide you with the information you're looking for.
I hope this helps, and please feel free to post back if you need further advice.
Cheers,
Brooks
