I don’t sync any apps via iTunes. If I’m setting up a new iDevice I generally just go to the Purchased tab of the App Store and kick off downloads from there. The one thing I do in iTunes that’s iDevice related is copy comic book files into the Comic Zeal app. But even then it’s getting less and less common for me to do that and more common for me to just open them directly from the OneDrive app.
Which is great as long as they are still available…
Never had that problem but I can see how it would be frustrating.
Edit: nevermind - read the rest of your post. 
I don’t actively sync anything via iTunes these days thanks to Apple Music. I do plug in every week or so to backup (encrypted backup to Mac rather than unencrypted backup to iCloud thanks) and to sync photos.
iOS9’s thinning feature has forced me to download via a computer too many times, for some odd reason updated programs which cross into the 49+ MB mark fail to update while on 3G/LTE/wifi… if you delete the program then redownload this glitch doesn’t occur again 
(if the program stores user data files, you’ll still need to upgrade via connecting to a PC/Mac–I don’t trust iCloud as it glitches every so often on syncs)
Lately I just use a older iOS 8.x device to download programs then sync.
iCloud backups are encrypted.
There is one other major issue, if an app for some reason gets removed from the app store it will remain in your library if you have it downloaded and you will still be able to install it on a device - you will not be able to do this if you do not have a local copy. I seem to recall one app that this is the case of for me - the game Bookworm
Incorrect. App Store - Updates (or Purchases on iPad) and then Purchased. Shows purchases that have since been pulled from the App Store (including Bookworm).
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Odd that Bookworm doesn’t show up for me in the purchases area then - hence my comment that I am please that I have the file in my library
OK, but it still doesn’t show for me - clearly there is something a little screwey with my iTunes account.
Quite possibly. It is iTunes after all.
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Is it possible you (a) bought with a different Apple ID or (b) aren’t signed in to the App Store?
Oddly after resetting network settings all apps are showing… including Bookworm, makes no sense whatsoever but oh well at least its back there now
There are some things which don’t show up after they have been removed. Stanza (ebook reader) is a case in point.
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Little bump for this thread. With the advent of iOS11 and itunes 12.7, you will no longer sync apps and ringtones via itunes. Well, you can still do it manually by dragging an app or ringtone from Finder onto your phone in itunes, but the actual sync functionality is gone. I wonder if the bell is tolling for itunes.
Could be. Apple wants us all to be streaming Apple Music with our infinite data allowances and infinte funds. Not for me. Seriously if iTunes (or other music apps for using your own music) disappear, so, probably, will I.
I stopped syncing apps long ago mostly because they were bloating up my HDD but mostly because it just wasn’t needed anymore.
I use Google Play Music I do still have some music synced from my iTunes library which is handy if I’m offline (which is almost never).
Ring tones… well I do actually have a few custom ring tones, all hand made, except one, and that’s the only one I would want to keep. My ring tone (since day 1 of the 3G) is the iPhone Ring from the original TV ad in the US. Why that isn’t a stock tone I don’t know. Seriously I’ve had the same ring tone (and message tone) forever… I’m old and like it that way 