We sympathize with the desire to reduce counterfeiting, but limiting the capabilities of new consumer devices punishes everyone while doing nothing to discourage determined counterfeiters. Anyone wishing to scan banknotes can easily do so simply by avoiding the latest generation in computer equipment. Instead of buying a cheap new scanner that performs poorly and is likely hobbled by CDS, buy an older used scanner that works on everything you throw at it. We highly recommend the Epson Perfection 2450 PHOTO which cost $400 when it was brand new, but now routinely sells for around $50 on eBay. This scanner is fast, has excellent color fidelity, and can even scan watermarks and security threads when used in film/slide mode.
If you already have a scanner that you like, but which refuses to scan some modern notes, you can likely replace the manufacturer’s provided scanning software with VueScan. This third-party scanning program works with almost all scanners and doesn’t prevent you from scanning troublesome notes. It costs $40, but you can try before you buy to ensure it meets your needs.
VueScan, and an Epson V39 are what I use. And GIMP when necessary.