I haven't tried since installing itunes 12.7 (the version that removes the App Store etc), but reports I've read suggest it still backs up everything with the notable exception of apps. These have to re-download from the appstore on the phone iteself presumably now. I'm assuming though that all app data is preserved (one would hope so!). Happy to be corrected if this proves not the case.

From macdailynews:

"iTunes backups are still there for iOS devices, but performing a restore won’t transfer your apps from your Mac, but will instead download them over the Internet from Apple, which is, of course, likely to be slower."