backup iTunes with iPhone 6s 128 gb

Hey jgcfromzeist,
You are correct in assuming that iTunes will ignore your photos if you have iCloud Photo Library enabled. It also excludes Photos that are stored in iCloud as well. Now one thing that could be taking up all that space is possible your messages. If you have an extensive list of conversations with attachments like pictures and videos that aren't in iCloud Photo Library, then that will take up that space. Take a look at the information below to go over the information on what iTunes backs up.
About backups in iCloud and iTunes
https://support.apple.com/en-us/HT204136

iTunes backups

From your Mac or PC, you can make a backup of your device in iTunes. Syncing your device with your computer isn't the same as making a backup.

An iTunes backup includes nearly all of your device's data and settings. An iTunes backup doesn't include:

• Content from the iTunes and App Stores, or PDFs downloaded directly to iBooks (You can back up this content using Transfer Purchases in iTunes.)
• Content synced from iTunes, like imported MP3s or CDs, videos, books, and photos
• Photos already stored in the cloud, like My Photo Stream, and iCloud Photo Library
• Touch ID settings
• Apple Pay information and settings
• Activity, Health, and Keychain data (To back up this content, you'll need to use Encrypted Backup in iTunes.)

Learn how to make backups in iTunes, how to find them on your Mac or PC, and how to delete backups you no longer need.

I would look at the storage on your iPhone to see what is taking up the space on your iPhone. Go to Settings > General > Storage & iCloud Usage > Manage Storage to see the list of items that are taking up space.
Check your storage on your iPhone, iPad, and iPod touch
https://support.apple.com/en-us/HT201656
Let me know what you find out.
Take it easy