Built an apk of my unity project, however the naninovel scene which works in the unity editor (the UI with NEW GAME, CONTINUE, SETTINGS BUTTON, do not show up) doesn't work. I have used Unity Logger and found out that Naninovel GameObjects don't even get Initiated.
Are there any build settings that I am missing ?

Enable Development Build in the Build Settings and post the logs here. If there's no mention of Naninovel in the logs then it's likely it's not related to Naninovel and is rather related to a project setting/custom gameplay in which case I suggest checking out the Unity forums for help.