You can currently have multiple Z-wave-JS integrations, there are multiple examples on the forum representing this and how to do it. The challenge is that only one Z-Wave-JS-UI Addon is supported natively, but you can install it on docker or other install methods outside of Home Assistant supervised.
I imagine ZHA will be the same, and I’ve seen a post in the ZHA section that they are working on allowing that implementation to run externally Zigpy developer(s) begun work on external and stand-alone implementations of ZHA - Configuration / Zigbee - Home Assistant Community (home-assistant.io)
Outside of those technologies, many integrations support multiple instances where that makes logical sense. For example, I have multiple Rokus and multiple Roku integrations.