You are correct, there should be no difference since it's pure data transfer but some people will always claim there is (see the whole cable debate) I couldn't tell with any of those that I tried.
My one big issue with one of them was not unsubstantial amount of jitter through any digital out (incl. AES/EBU!) even with the latest firmware, requiring a DAC with user-adjustable jitter correction. That should not be the case, esp. since it was pretty pricey... So whichever you choose, check some reviews regarding that.
That one, the CA iD100, also has a USB port but it is strictly for convenient syncing with a computer, not audio transport. I don't know any other that does. I looked at the Wadia too, didn't see any indication either.
Keep in mind that the old dock connector is being phased out in favor of the new lightning connector, so I doubt there will be much innovation (like USB audio). Also, full-on iOS devices (iPhone, iPad) offer very poor remote control support regardless of the dock make/model.
My recommendation is the Pure i-20, probably the cheapest pure digital one, yet also the most stable & reliable I have tried! Again, since we're talking about simple data transfer, not really any sonic improvement to be gained from going with the more expensive ones anyway. If you can live with the somewhat goofy pedestal design. As a bonus, it offers digital remote-controlled volume (*) if your amp/DAC doesn't offer that. And analogue line-out in case you have an older amp to hook up to, or a portable system for a party or similar. The remote is kinda chintzy, but I replaced it with a simple, nicer programmable one.
(*) In case you are one of those people worried that it will deteriorate the digital output: it has been discussed (and apparently confirmed by one of their engineers) that at max. level it is the original, full bit-width signal being piped through.