The iTunes 12.6.5.3 version will only work in Sierra and High Sierra, that is why your iTunes updated to 12.9.5.5 as you went to Mojave. And yes it does not support App downloads or updates into iTunes anymore.
However don't bother going back at this point, because the iTunes 12.6.5.3 version in Sierra/High Sierra has been broken since March 17th or so. Many of us have petitioned Apple support in various ways and on several threads here to bring it back online, but so far NADA.
March 18th was the debut of Music app to replace iTunes for the more recent versions of OS for Mac, the support agent I talked to said that is likely why iTunes 12.6.5.3 version is no longer working. I was also told backing up devices thru the Mac now will be done in Finder since iTunes has disappeared and Finder will NOT include copies of all of our iOS apps. So good luck rebuilding any old devices without long wait times to download your apps over the internet......
For now I am checking each of our iOS devices( we have 5 active phones and ipads) in the app store every couple days to be sure they have latest updates, apparently that is all we have going forward.