icloud only backs up apps, not data in the apps

Check at Settings > [name on top] > iCloud > Show All. If an app is listed and the switch is turned off, then that data will not be backed up to iCloud. Not all apps will use iCloud to store data and that is up to the developer of the app.

You are in control of the data that an app backs up. This can be checked at Settings > [name on top] > iCloud Backup > [name of device]. You can switch off what you do not want stored in a backup. Some users prefer to reduce the backup size and choose not to backup all data. The choice is yours on how much data you want backed up.

Using iCloud for storage is different than the data that is stored in your Backup. For example, if using iCloud Photos, then your photos are not stored in the backup file and are instead stored in iCloud to be available for other devices that you may want to view that data.

It's really not that difficult. The developer of an app can give you an option on whether you want to store data on your device where it will be backed up, if you have allowed for that at the previous link, or stored in iCloud where it will be available on all your devices, but to avoid duplication of iCloud storage, it is not included in your backup file when the data is stored in iCloud.