Ffmpeg is totally capable of doing this. Something like ffmpeg -i in.mkv -vf "crop=width:height:x:y" out.mkv might work. You would need to specify the crop area (x:y), which you can get with ffmpeg's cropdetect. Here's an article about it. To automate this, I would use a for loop in a shell script, for more control, or just a one liner if width, height and x:y are the same for all:

for file in *.mkv; do ffmpeg -i "${file}" -vf  "crop=width:height:x:y" "cropped_${file}"; done

Handbrake has the option to autodetect black bars and crop them out. But you have to reencode the file, unfortunately.

Besides modifying the file, mpv can also automatically crop the videos with their autocrop script while playing: https://github.com/mpv-player/mpv/blob/master/TOOLS/lua/autocrop.lua

I use it for playing 21:9 content inside a 16:9 video file on a 21:9 screen.

Kinda unrelated to the question but i was actually looking for a linux native way to convert blu ray audio discs to seperate flac audio tracks after ripping them with makemkv. I could only find ffmpeg which seemed a bit daunting to me, but it looks like mkvtoolnix might be able to do what i want.

https://ffmpeg.lav.io/

MKVToolNix has a great cropping feature that completely lossless because it just writes an information into the file how many pixels to leave out.

The massive problem since quite some time is that I'm not aware of any media player respecting this. VLC used to support it but a decade ago suddenly stopped: https://code.videolan.org/videolan/vlc/-/issues/13982

If you have the originals, maybe encode them again. HandBrake has a nice preview feature.