I recently (about 3 weeks ago) posed the UV cut vs. non UV cut question to X-Rite, asked about why the options were there, etc... This is the story as it was told to me... The i1 Pro is originally a Gretag MacBeth product and they chose to do UV compensation in software. When X-Rite bought them they had a different philosophy... they wanted to filter out the UV before it got to the sensor and not rely on software to do that (although I have to say I seem to remember a UV cut option being there prior to the GMB getting bought by X-Rite... (shrug)) so the UV Cut option was born. Of course the software still had to support the existing i1 Pros out there so the option still had to be present in the software.
Now... the problem is if you profile a paper with OBAs without a UV filter, the UV can potentially throw off the profile so the UV filter is a necessary thing (be it a physical filter, or a digital one). I then asked "What will happen if I profile a paper WITHOUT OBAs using a puck that has a physical filter?". In this case there is no UV content so there's nothing to filter. The end result is the same as if there was no filter there. That said I decided to go with a puck that had the UV cut and so far I haven't noticed any issues profiling non OBA paper such as Hahnemuhle German Etching. When I profile papers like Epson Exhibition Fiber the UV filter is of course already there.
Now... that filter IS of course a physical filter and any addition of an element is going to impart some kind of distortion. In this case I don't believe it's as critical as we aren't concerned about things like sharpness so the question then would be, is the physical UV cut filter detrimental to any part of the process when it is not needed? I believe the answer is no.
If there is anyone in the Boston, MA area with an i1 Pro without the UV cut filter, get in touch with me. I'd love to do a side by side comparison.