I’m using the portable version of Sublime Text. And I guess the license information is also stored inside the Sublime Text folder itself. If someone copies this folder, they’ll be able to use Sublime Text licensed. Is there a way where I can protect my license key from being misused like this?

Not if you let them copy the folder themselves, I don’t think. If you’re giving them copies, you could always run the copied application and remove the license before sending it to them.