I've fixed this issue to my satisfaction. I converted the driver to use Microsoft's built-in USB driver, which is signed, and built Jaron Viëtor's Linux command-line tool in Windows to access the new driver. I've attached the tool to this post.
You need to have installed EMS's driver first and upgraded the firmware to v3.05 using the Windows driver and tools from http://www.hkems.com/download%20-%200907.htm - note the Linux/Mac option and the author's Github at the top, it's this source code that I compiled in Windows.
For anyone having problems disabling Driver Signature Enforcement, this is the only way that worked for me:
To disable Driver Signature Enforcement in Windows 10, go to Start > Settings > Update and Security. Select Recovery from the list on the left hand side and then click the Restart Now button under Advanced start-up. Then click Troubleshooting > Advanced Options > Startup Settings and then click the Restart button at the bottom right. Your PC will restart and give you a list of options, press F7 and Windows will start.
Once you have installed the driver and upgraded the firmware, you can use EMS's NDS_Adapter_Plus_V3.03.exe tool to access your device. The problem is that when you reboot, Windows will block the EMS driver until you do the steps in the previous paragraph again. If you can't use command-line tools or the Windows Command Prompt, stop here because you won't be able to use EMS's tool anymore if you continue with the rest of this.
Reboot your PC to re-enable Driver Signature Enforcement.
To fix the driver you need a program called Zadig from http://zadig.akeo.ie/ - the version for Windows Vista and later is what you want. Download zadig_2.2.exe and put it somewhere you can find it. Plug in your NDS Adapter Plus. Double click your zadig_2.2.exe and select the Options menu and List All Devices, you should see an entry called EMS Inter-Link Cable, select this and then select "libusb0 (v 1.2.6.0)" in the box to the right of the green arrow using the fiddly little buttons and click Replace Driver.
Now you can open a Command Prompt and use ndsplus.exe to read and write save files without having to disable Driver Signature Enforcement. Enter "ndsplus -h" to get a list of the options, or use "ndsplus -b savefile.sav" to backup and "ndsplus -r savefile.sav" to restore.
EDIT: It might not detect the save file size properly in Diamond/Pearl/Platinum, don't know why. Just add "-s 524288" before the "-b" or "-s" switch to force it to copy 512KB.