As
@Ableza already said, MPLAB X is an IDE (integrated development environment) provided by Microchip. It can be used to write firmware for their microcontrollers with. It can also write ("flash") that firmware to these microcontrollers.
To be able to do so, it needs to communicate directly with certain programmer/debugger hardware via USB.
MPLAB X is essentially NetBeans with a few custom plugins added to it. NetBeans, in turn, is a programming environment developed by the Apache Foundation. It is written in Java and designed to run on all kinds of different operating systems without the need for much operating system-specific code, if any. "Build once, deploy everywhere" is what they like to call this principle. To accomplish that, these frameworks are usually designed to weasel their way around as many operating system functionality as they can. So my theory is that they access the USB ports as close to the hardware layer as they can get away with, and they might end up locking something up that macOS would otherwise manage for them if macOS's USB APIs would be used as originally intended.
Something similar applies to Roon. It, too, is designed around one of those "build once, deploy everywhere" frameworks (Microsoft's Mono/.NET in their case). And it, too, needs to have direct access to your USB ports. One of Roon's core features is the Roon audio pipeline. The entire purpose of that is to control every layer your audio data has to travel through to get to your DAC, so that they can ensure that no unintended up- or downsampling or some other form of conversion happens. For that, Roon needs to be able to communicate with the DAC directly, not through macOS's general audio pipeline. And so they, too, will try to hook onto your Mac's USB ports as close to the hardware as they can get away with.
My theory is that Roon does this in a somewhat cleaner way, meaning without blocking ports that it didn't find a DAC connected to. MPLAB X's behavior seems to be less considerate in that it apparently keeps blocking the ports in such a way that it renders Roon incapable of discovering any connected DACs.
MacOS itself seems to be unaffected by all that, by the way, because the OS still discovers connected USB devices just fine, and DACs still work when the default audio pipeline of the OS is used.
There's a lot of guessing on my part involved with the above. I didn't have the time nor the inclination to dig much deeper into what exactly caused the issue, but based on my own knowledge and experience with these things I'm relatively confident that I'm not too far off the mark with this.
Whether or not my assumptions are correct, none of the above is really relevant to what you are experiencing anyway. Neither MPLAB X nor NetBeans are shipped with macOS, you would have to install either of them deliberately.
But the cause is probably still similar.
My guess would be that you have something installed on your Mac that either meddles with your Mac's USB ports or (more likely) something that hijacks macOS's audio pipeline. A lot of people use software by Rogue Amoeba, for example, to reroute their audio pipelines for some reason or another. Airfoil, Loopback, Audio Hijack, SoundSource … all of them are designed to hook into and meddle with macOS's audio pipeline. And while I'm sure that a lot of people are happy with the results, I always found that these applications cause more problems than they solve.
So my first step would be to check if you have anything like that installed on your mac and try to uninstall them as cleanly with as little residue as you can. With apps like these that try to inject themselves as far into the OS as they can, a simple delete of the app bundle is often not enough, so you'll probably have to follow a tutorial or two to actually get rid of everything.
If that doesn't help, the next step would be to check if you have any other software installed on your Mac that requires a connection to specialized hardware via USB.