They decided to remove a vehicle that wasn't glitched, and could be found and claimed by completely normal means. I'm guessing they only removed it because it was a rare and unique vehicle, not because it was modded, because it wasn't. They only want you owning unique cars if you buy them from the in-game website.
This is a perfect example of R*'s ironic fallacy. This is supposed to be a "revolution in open-world multiplayer" as they put it, yet ever since GTAO launched all they've been doing is dictating the way they want you to play. From nerfed cash payouts, removing replays, encouraging you to buy their cash cards, and now removing your rightfully owned vehicles.
"You want your unique truck with tons of awesome customization options that you can show off to your friends, that you rightfully found, claimed and likely spent thousands of in-game money customizing? Well too bad, because WE don't want you to have it."
I can already see it now. R* is going to charge you for a "Rare Vehicle Pack", which includes vehicles such as the Rat-Loader so they can make some extra money off of something that's already in the game. They're becoming just as bad as EA, Activision, and Capcom.