As far I understand, the simulator is not just as the Android emulator, so you do not deploy something into it, because it is the application itself, even in the apparent form of a device running another application.
Said that, it is a minor issue for sure, I have not any problem closing the instances manually.
In the long run you have to take into account that developers will end up having a lot of instances open on the system for sure, because of the normal tendency to forget and being busy and distracted. Very soon closing the instances is felt as a chore, not even mentioning when the instances have some conflicts, as said in my original post. Furthermore I use very often (even several times in a minute) the "hot corner" function that shows me all windows, and it is easily crammed by the simulators.
I think that the "Stop" function is triggerable from the plugin, calling it in the run/debug initial operations. It would depend on the "only one instance" option in the settings. It closes the opened simulator, I tried. "Stop All" closes all instances. With appropriate combination of settings a developer can decide to mantain some instances open, if needed, while the most recent is closed and re-run as the "active" one.
Regards