In Unity 5, the Plugin inspector was introduced:
http://docs.unity3d.com/Manual/PluginInspector.html
Basically, it eliminates the need for the Assets/Plugins folder.
Before, in Unity 4, we stored ALL versions of our plugins (Debug, Profile, Release) in Assets/Wwise/Deployment/Plugins. When you installed a specific configuration, we copied it over to the Assets/Plugins folder, and this is the plugin that ended up in the game.
Unity 5 has no need for the Assets/Plugins folder any more; we simply need to check the correct checkboxes in the Plugin Inspector. This means that all our plugins can stay in Assets/Wwise/Deployment/Plugins, and we have a script to activate the correct plugins.
In your case, I think it is safe to say that you can simply delete the AkSoundEngine plugins that are found in Assets/Plugins, and then, using the menus, go to Assets > Wwise > Activate Plugins > Profile. The only place the Wwise plugins should be in your project is in Assets/Wwise/Deployment/Plugins.