Why are hardware-based manipulations, like black and white photography (traditionally using black-and-white film), long exposure, etc., which also result in an "unnatural" image, acceptable while software-based manipulation (like HDR) is frowned upon by the photography community?

Differences from human perception that are due to limitations of the medium are generally more accepted than intentional alteration that is free from such limitations. Obviously, there's a range of opinion, but this isn't just a "some people think" thing because there's a difference between outcomes which feel, for physical ("hardware") or historical reasons, natural for a particular art form and those which don't.

• Black and white photography is not a "hardware manipulation", even if we consider film to be "hardware". It's a historical technical limitation, and because of its history, has become part of the language of photography.

• Long exposure — I'm assuming you're thinking of the smooth-as-butter waterfalls, or traffic as streams of lights — may not exactly match human perception, but neither does short exposure! The human visual system builds an always-updating, time-based model of the world. We don't see a stream (or cars!) frozen in time. Any shutter speed selection results in something that is an artifact of the photographic process.

Similarly, one might find visible brush strokes in an oil painting made with physical brushes to be fine while adding brush-stroke effects digitally to be "frowned upon" — even when the digital result looks amazing.