When apps go missing but you know they're installed it could be because you've set them to 'protected' which is a feature of Cyanogen. To get them back, tap options while on the home screen then the three dots above 'widgets' and tap Protected apps (highlighted here in yellow):
This may present you with an authentication challenge such as a pattern or pin code, enter whatever code you may have set to get past it. Once at the app list you can scroll through and untick the apps that have become hidden so they appear in your regular app list again.
This can be a very useful feature, especially if you occasionally share your phone with people and don't want them accessing certain apps such as online banking. For example, if you wanted to lock out specific Google apps only you can get to them, you could group the icons on your home screen and protect the entire group in one go by tapping the padlock (highlighted here in yellow).
To remove the Google search bar at the top of your home screen tap the options button while at the desktop and select the three dots above "widgets" then turn Search Bar off (highlighted here in yellow).
The OnePlus uses Cyanogen so this should be the same for any device that also has the same OS version.
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