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If the shrubs were mine, I'd wait until spring, and give them a light shearing. This will promote new growth to fill out the thin spots. I've attached an article that should help: https://www.gardeningknowhow.com/ornamental/shrubs/boxwood/trimming-boxwood-bushes.htm

Boxwood, buxus, is best pruned mid-March IMO. Pruned just before flushing will eliminate bare stems and thin spots during the winter. this article should help: https://www.gardeningknowhow.com/ornamental/shrubs/boxwood/trimming-boxwood-bushes.htm

Some people say they can smell a urine scent coming from boxwoods. Others don't. Had a friend that couldn't stand them, I've never been able to detect any scent.

It depends on many factors. Here is an article on boxwood care:
https://www.gardeningknowhow.com/ornamental/shrubs/boxwood/boxwood-care.htm

It could be a fungus but it also be a lack of sunlight. If the shadow from the house fell just right, it could cause a patch like this. But, since it is new, we can assume that it is a fungus. Treat the plant with a fungicide and that should help clear it up.

You can prune back the holly by about 1/3 without hurting it. Any more than that per year will hurt it. As for the boxwood, you can replace it with another boxwood, but they are slow growing shrubs. It may take it some time to get to a size you would like. If you decide to replant boxwood, wrap it in burlap in the winter to help keep it from harm. You might try looking at Inkberry. It has a similar look to boxwood. It grows slowly as well, but is typically a little more cold hardy than boxwood and can take the winter better.