I just checked, I still have the mobile applications folder inside the iTunes. I would hold off deleting the application folder for awhile unless you need the space, in case apple reverses course or creates a stand alone app for the mac like they did with iBooks. (Also, it may be the last way to get ahold of an iOS App to manually load it using the instructions below.)
I think only the original phone didn't have an app store, although it was updated in iOS 2/3 to include one. As far as I can tell, apple wants you to either use the iOS app store on the device itself to download the last compatible version (if the app maker has set up the app to allow it) or you can manually add the old app if you have the actual app file still on your mac/pc iTunes library via the instructions included:
https://support.apple.com/en-us/HT208075
https://support.apple.com/en-us/HT201593
Manually add items from your computer
If you have media on your computer that you can't
redownload from the App Store or iTunes Store directly on your iOS device, such as custom ringtones or iOS apps, you can drag and drop the media from your computer to your iOS device using iTunes.
- Connect your device to your computer.
- Open iTunes. Make sure that you have the latest version.
- On your computer, find the item you want to add to your device. If you're looking for Apps, Tones, or Books (for Windows) that previously appeared in your iTunes library, you can find them in your iTunes media folder.
- Drag the item from your computer to your iOS device in the left sidebar of iTunes.