generally for msbuild, the dependency tree is defined by nuget packages added. each nuget package has a list of other packages they depend on. if a project reference is added, then the project file has the dependencies.
some packages dynamically access their dependencies at runtime. for example ef core does require any database drivers at build. these are discovered at runtime via the connection string. the app generally adds the nuget package of the desired drivers so they will be included in the publish.
so if your plugin dll requires other libraries, they should be included with the plugin and copied to the bin folder. you probably want to define a dependencies type file for the plugins. your code will also have to resolve if two plugin have conflicts.
the optional myapp.deps.json is used by the pack/service installer. if you are making use of this, when you add a plugin, you need to add all its dependencies. that is you need to patch before your app is installed,