I'm a Canon shooter, not Nikon, but I won't hold that against you. I've been carrying SLR film cameras and then D-SLR cameras for almost forty years. I've carried them up and down mountains, through the snow, and even on ultralightweight backpack trips.
You have to decide one thing first. Are you going to need to keep it out and halfway ready, or are you going to keep it protected in the top of your pack? Either way, there are compromises. What I've used for about 13 years now is a so-called camera holster. If I am in ugly weather or ugly terrain, I can keep it all in the top of my pack. However, if it is decent weather and a pleasant trail, I will have the camera holster hanging on its shoulder-neck strap, so it will be riding somewhere around the top of my right pants pocket. If a wildlife target pops up, I can have it out and shooting in a matter of seconds. I have a short holster if I am using a short lens (<200mm). Then I have a longer holster if I am using a longer lens (<400mm). For a lens longer than that, it won't be in any holster, and it will be on a tripod unless I have it in the big Lowepro lens case. Most camera holsters are somewhat flexible on the outside, but they have a semi-rigit plastic shell inside to protect the equipment. Most have a semi-weatherproof top lid.