Well, plugins don't *have* to run constantly. They are bits of code that only run when a command is given. If that code is just a quick query to a website, read a file, or somehow a hand-coded, high-availability database for NASA, that's up to you
In a nutshell, plugins do absolutely nothing until they are told to do something by VA, and VA doesn't do anything to the plugins unless a command is issued. Same goes for inline C#/VB.net functions. Ideally, if a plugin is going to continue running beyond the scope of a command, it should be designed to be able to be stopped if the user needs it to. If you need EDDI to stop, you'll need to issue the right command to it to stop doing whatever its doing if that functionality exists. Otherwise, you'll need to ping the EDDI author to see if that can be done for you in that regard. Also, the plugins themselves can monitor what profile is active, so if they are running outside where they should be, they have the ability to limit themselves. So, effectively, the onus is on the plugin developer to keep things square.
Hope that helps!