Are low profile nuts okay for my first 5-inch drone?

As long as it doesn't come lose during flight, it will be fine. Check every nuts before flight so that you won't crash your expensive quad mid flight. 

The important part is that they are lock nuts. This way it's way harder to loose them. But of course check them before flying, so you can be sure that they are secure..

Thread protrusion is a good thing. No threads in view is not so good.