If you expect her to use it, you also have to expect that it will have to be washed a lot, especially since baby might make messes on it, so it needs to be very durable .... sounds like you already know this

Not sure if you do this or not: but the first thing I do with any fabric that comes into my house is wash on hot, dry on hot, iron on hot. I suggest doing the same thing with any embroidery thread you plan on using; you can do it by hand, but agitate a lot and try to 'abuse' it. Just to make sure everything shrinks and bleeds as much as possible before you use it.
I've never used nylon thread so I can't speak to the durability of it, but good quilting cotton does hold up well.
I love that you're thinking of the symbolism and meaning you'll put into it, that is so sweet and thoughtful!