I'm not a pilot but I think I've tried enough contact lenses to give an educated answer to your question (working with an optometrist who is a contact lens specialist does help).
Personally I think the Focus Dailies Aqua Comfort / Acuvue Moist is more of a gimmick then giving me a better time with CLs. My eyes dry up at night and sometimes I have difficulty blinking with my CLs, which is the same with the non-moist counterparts.
Obviously it'll depend on what type of eyes you have - I've had patients come back and say they love the moist CLs so much, they don't mind paying an extra few dollars for the moist version. Then there are ones who absolutely detest the moist CLs, and specifically request for the non-moist ones.
However, rumour has it that Johnson & Johnson will phase out the non-moist 1 Day Acuvue CLs w.e.f. end of this year, and Ciba Vision with the non-moist Focus Dailies in the near future. I wonder how those non-moist CL loving patients will cope. Even though I said moist CLs haven't changed my life substantially, I'm not fussed either way, moist or otherwise.
But I guess the uber-dry environment in the aircraft would dry your eyes out anyway, so it might pay to have those little tear drop packets that you can carry onboard safely i.e. Bion Tears or the like (the brand names elude me).
Hope this helps.