We looked into this before at my company, but my java fu is weak and we dropped it in favor of doing the usual programming bar codes for scanners using the Zebra 123 config utils.
The Zebra APIs can be downloaded from their site and for Java follow the JPOS standard. I have not looked to deeply, but the sample applications for Java in the SDK are just JPOS library examples, there is nothing specific from Zebra in Java… I do not think there is much you can do in the way of doing scanner config with Java as most of their API uses WMI or .NET for those type of functions.
What type of “modifying the scanner from Ignition” do you want to do. If you provide some more details that might be helpful, there are a few of us on the forums that do a lot of barcode scanner and label printer work with Ignition.
PS - The only super nice thing that would be cool to do with the Java API would be to access the Image Capture functions of the scanners to do document scanning. This would be great in Vision, but with Perspective, the UX for doing this with a Tablet/Phone is much better IMO.