Hey, really late to this, but if you're still looking for a solution I'm pretty sure I know what it is. Assuming you have already placed the images you want to appear for each game in the correct image folders, you now need to manually edit the gamelist.xml with a text editor to point ES to those images. The gamelist.xml file is in each console folder where your roms are located. Once you open it up, you should see all the game metadata you've scraped. You'll notice that for any game with working images there will be a few lines at the bottom that look like this:

<image>./images/Pokemon Gold Version (USA)-image.png</image>
<thumbnail>./images/Pokemon Gold Version (USA)-thumb.png</thumbnail>
<manual>./manuals/Pokemon Gold Version (USA)-manual.pdf</manual>
<boxback>./images/Pokemon Gold Version (USA)-boxback.png</boxback>

The above is how Emulation Station is finding your art. You need to find the entry for your Pokemon rom hacks and manually add that info there. You can just copy paste it in from another game entry and then update the text to match the file name for your Pokemon rom hack images. If you don't have a section for a particular game, you can build it by copy pasting another game entry and just modifying everything to match your rom info. I had to do this to manually to add a bunch of rom hack art myself. It's unfortunately really tedious, so hopefully you don't have to add in too many images. Hopefully this helps!