If you can't find your apps in Android Auto's app launcher, they might be temporarily disabled. These apps might still show up on the screen, but won't show up in your Android Auto app launcher until you re-enable them.
Go to Settings, and select the App that is missing to open 'App info'. If the app is missing, then it must show the option 'Disable' in the app settings. You should enable it.
Still, if apps disappeared from android home screen, then there is a possibility that the apps might be hidden.