Destroy your "pimped out version". You can keep taking it out. That's what I did. I had about 20 left for the challenge or so and just spent a while taking the same emu out of my garage and destroying it. It isn't lost.
If you're concerned it may not work, store the next regular one you find and do it with that one instead.
After you buy the Let's Pretend store (or maybe even before you buy it), you'll eventually get a survival mission call to stop mascots. They drive up in Emus, Knoxvilles, and Widowmakers, and you can get a huge chunk of Emu and Mascot kills from this activity, maybe even the full amount if you are quick at destroying them.
The southern most are of the island with Shaund's crib. The theft of an Emu sends you there as well. Also as previously mentioned, the protection deal against mascots after purchasing the dress up store.
Thanks for the reply. I already did the mascot survival and most of them showed up in those golf carts instead. I already beat the game at 94% and only 2 challenges left. Emu one and the human torpedo (still trying to figure out how that one works).
I wandered the southern area near Shaundi's crib and they are not spawning fast enough. I should just blow up my own instead. I actually like the smart cars in this game. Once fully upgraded, it's pretty fast and handles well. I also like how it rolls around like a ball if it didn't land right after a jump. Maybe I should buy one for my mother on her birthday...
Someone said this above, but play Tank Mayhem on hard and you'll get to blow up a lot of Emus.
If you want help on Human Torpedo... look below ("spoilers")...
Human Torpedo is bailing from your car as it's speeding. It's kind of unresponsive, so try and aim your car for a wall down a straight road and bail a hundred feet or so away so the car hits the wall with maximum impact. The airport is probably a good place for it, just be sure you can replace the car quickly if you blow one up.