You're going to have some degradation, but it's just one of a number of factors, and it less importnat than the mics, placement, sound in the room, etc. The issue is more the A>D in the JB3 than the A>D>A in the UA-5.
As far as the cheap optical input on the JB3 goes, it's a double edged sword. Field recording like we use it for is NOT what the JB3 was designed for. The optical in is plenty sturdy enough to do what it was actually designed for. Plus, keep in mind that if the JB3 weren't cheap, it wouldn't be inexpensive, either.