Ideally what I'd like to do is add a shortcut to the iPad keyboard that launches another program and in my case a scanning application.
We'd like to utilize the iPad camera as a scanner and whenever we tap a text input box in any third party application, have the ability to launch the scanner software, scan the code and place the scanned data into the text box.
I've read about the scanning libraries and using actual barcode scanners, but I haven't seen anything that would allow you to create this type of shortcut.
Any thoughts or suggestions on where I may find more information?
tl;dr: It is not possible.
The iPhone keyboard is cannot be modified system-wide or replaced. See the 4th question on the Fleksy FAQ
As you mentioned, your options are:
If you don't have access to the application source or can't convince the developer to add scanner support, your only option here would be to use a stand alone scanner app, switching between apps to copy-paste the scanned data into the text field.
Pros
Cons
It is possible to integrate a barcode scanner into an app using the provided SDK and that is advisable for most applications, but a lot of scanners also support HID mode. In HID mode, the scanner connects to iOS (or Android) as a keyboard and can "type" into the active input field.
Pros
Cons
Disclaimer I work for Socket Mobile. Socket Mobile makes beautiful bluetooth barcode scanners.