easiest solution would be to buy a rear emblem off someone who's running the JDM emblems. I've seen stuff in the past where users bought rubber plugs at hardware stores, and then painted the plugs to the closest color of their paint. It's not going to be 100%. Having a body shop do it will run around $300 from past threads I've read. They'll weld the holes shut, grind it all down, and then repaint the trunk. I've seen people mention bondo in the past, but others claim that it cracks over time, and the paint never matches quite right with the rest of the trunk.
1 - replacement emblem
2 - run jdm emblems
3 - try a plug / paint
4 - body shop repair
just depends on your budget, and how bad you want to have your emblems gone. I've also seen people paint their "H" emblem the color of their paint to make it basically disappear.