Yes, for some suede it is. Your shoes are ultra rustic, so I don't find what you've identified out of keeping with their general aesthetic, and it wouldn't both me. Shoes are meant to be worn, and wearing inevitably leads to signs of wear. Obviously suede with longer and/or softer nap will be more prone to this.
If it really bothers you, you could acquire a pair of mustache scissors, which are small, sharp scissors designed to allow you to very precisely snip off an errant mustache hair, but which serve equally well for an errant bit of suede nap. But should you elect this, please be careful!