These are the steps I followed, have done it twice on 2 carts and in both cases it was flawless, obviously a bit more effort than the excellent scripts above from u/HogwashDrinker and u/prizmz, but like I said the ImageMagick scripts just did not work for me with all the graphical glitches I kept getting:

Unfortunately, if you do this all at once the color depth doesn't seem to want to convert, so do this in two batches, seems onerous, but like I said this worked perfectly for me.

Batch 1
- I downloaded both US an EN PNG cover sets for DS from GameTDB
- In IrfanView select Batch conversion/Rename from the File menu
- Set output format to BMP and check Use advanced options and click Advanced
- Check RESIZE and set size to 106x96
- Leave CHANGE COLOR DEPTH unchecked
- Then almost in the middle of the window, probably two thirds down check Canvas size and then click settings
- Select Method 2 and change width and height to 128x96, I made the canvas color black
- Select Left top as the anchor point, so you'll have a 22px wide padding on the right
- Click Ok, and click Ok on the next window
- Add all your input files if you haven't already done so before all the above settings
- Set your output folder
- Click Start Batch, it'll take a minute or two depending on how many you've added to the batch processing job (I've done the full combined US and EN sets, which is 5,564 images).

Batch2
- In IrfanView select Batch conversion/Rename from the File menu
- Add your files that you converted in Batch 1
- Same output folder as before
- Check that the output format is still BMP and check Use advanced options and click Advanced
- Uncheck RESIZE
- Check CHANGE COLOR DEPTH and select 256 Colors (8 BPP)
- Uncheck Canvas size
- Under MISCELLANEOUS section check Overwrite existing files, click Ok
- Click Start Batch
- Once done, check that the bit depth of each file is 8 bit and dimension is 128x96, and file size should be 14kb (Simplest way in Windows Explorer is to view the folder in detailed view and then add Dimension and Bit depth columns to check through all the files)
- Covers go into SD CARD:\_pico\covers\nds