If the platform specific .json of plugins was removed, cordova prepare command doesn't re-create it, and as a result doesn't add plugins since 6.3.1 version, 6.3.0 is okay.
[UPD] more detailed steps to reproduce:
- install firstname.lastname@example.org
- go to project with platform and plugins installed
- do cordova platform remove android (or ios, doesn't matter) -> platform is removed, <platform.json> file is removed
- do cordova prepare -> platform is added, <platform.json> is recreated, therefore plugins are added to the fresh created platform.
- install email@example.com
- do same steps
- on a last step the <platform.json> is not recreated, therefore platform is created but no plugins are added.