The lens hood one is a bit of a strange one to be annoyed at. I do this purely out of laziness. I can’t be arsed stopping and fishing it out of my bag if I need it for a shot. I quickly just change it around and have done since the 90s when I started. Why does it annoy you?
A lens hood is not just optional, if it is the original one which came with the lens it is carefully designed to keep the image circle clear while obstructing light rays which hit the front element at small enough angles such that the refraction index of the glass causes them to diminish contrast.
Whether outdoors or inside under artificial lighting, the hood will improve (micro)contrast and through that, sharpness. It will also allow more accurate exposure readings, especially when using a flash by not allowing environmental lighting to hit the lightmeter.
A decent hood has a certain degree of stiffness/elasticity to it which will diffuse energy in a fall or bump not dissimilar to the crumple zone in a car. and also protects the front element from being accidentally touched.
You've changed the original question from it being a "pet peeve" to an "annoyance" and having it reversed while shooting to just having it reversed in the bag (which makes sense) so I cannot say it annoys me. I It rather tells me the person behind the camera cannot be arsed to...oh well, you said it youself.
In the bag: reversed for storage. The moment the camera comes out: put it on as it was meant to, that's all.
Sure: pet peeve = a minor annoyance