Hey, Everybody! Trademark Doesn't Work Like That!They didn't call Dash "Firefly" because they didn't have an active trademark on the name. Furthermore, they couldn't claim trademark on the name because they let it lapse sometime long ago.
That
doesn't mean they are prevented from making a new pony toy and calling it "Firefly," though. It also doesn't mean they don't have any trademark rights if someone else tries to make an identical toy Firefly and sell it. It just means they can't have a
registered trademark for "Firefly" as a pony toy anymore- meaning they can't use the little ® symbol next to the name on the packaging. They can still use ™, though!
Also, Joss Whedon's space cowboys don't have anything to do with it. Science fiction and kid's cartoons are not the same thing, and you can trademark the same name for two different things, as long as they're not in the same line of business. For example, Delta Faucets and Delta Airlines are completely unrelated companies. You don't walk into your local giant home-improvement store and think "Hmm, am I buying a faucet or getting tickets with a connecting flight in Atlanta? I JUST DON'T KNOW I'M SO CONFUSED

"
So: Hasbro wanted pony names for G4 that they could hold registered trademarks for. They either invented them (Twilight Sparkle) or reused recently-used names that they already had lying about (the rest of the 6, Scootaloo, Cheerilee, etc.)