It looks as though things with Nemo may not be quite as certain as they seemed. When I spoke with the vet Monday evening, she explained that for cats, having a hyperthyroid condition has a protective effect on the kidneys. However, it's bad for the heart and other systems, so we medicate to bring the thyroid down, which removes the protective effect and leaves the kidneys to cope on their own.
We've been having trouble getting his thyroid meds dosage right — started at 1/2 tablet a day, which wasn't enough; moved to 1/2 tablet twice a day, which wasn't enough; moved to 3/4 tablet in the AM and 1/2 tablet in the PM, which was too much; moved back to 1/2 tablet twice a day. Apparently that's still too much; a normal feline thyroid level is .8, she said, and Nemo's measured .2 — far too low. So we're decreasing the meds back to 1/2 tablet a day.
Because his thyroid level is artificially low due to the too-high medication dosage, she isn't sure whether the kidney results they saw are actually there, or are also artificially induced by the meds.
Of course, she stopped far short of saying "it's not a problem" or even "it's probably not a problem", but I'll take "I'm not sure if it's really a problem or not", gladly.
So now I'm off to the vet to drop off the urine sample, which should help give more information. Also going to pick up the new low-protein cat food (poor baby).