sxhkd

Some tiling window managers work this way without any issues. Bspwm[0], for instance, uses a client CLI program (bspc) to send commands to the daemon and alter its configuration at runtime. In fact, it doesn't have a configuration file format at all, since it can be configured via a simple shell script that runs a sequence of bspc commands. It also doesn't have any key binding functionality and offloads this to a separate program, sxhkd[1], whose only purpose is to interpret key presses and execute shell commands. Since this is bspwm's interface, the two work seamlessly together, even though they're not dependent on each other at all. This is just brilliant design, and speaks volumes for the "do one thing and do it well" school of thought. For the record, I've been using both programs without a single issue for the past 3 years at least,

On Linux it depends on your desktop environment, I suppose. Or if you just use a window manager, like i3wm for example, you can define all sorts of hotkeys, which you can also bind to custom shell scripts, or anything you like, in your i3 config. Edit: I used this a while ago, when I was using bspwm as my window manager: https://github.com/baskerville/sxhkd