Well, they're different games, and so work differently. In JJ1, all the enemies and other objects are defined inside the level file. So one level might have a normal carrot object worth 10 points, another might have it be worth 2000 points, and another might have it spin around in a circle until collected. And so on. Graphics are defined on a per planet basis, so while there's a limit on how many sprites can be defined at once (and how large they can be), you can in principle import any sprites you want. As for defining those objects, there are no "scripts" as you put it... JJ1 has a list of ~60 behaviors (how objects move around) and ~40 modifiers (what happens when you touch or shoot the objects) which can be combined and passed various parameters to behave in certain ways. I'd recommend downloading J1E and having a look for yourself.

As for JJ2, well, I think we're all familiar with how JCS works. But if you want to see custom enemies and things there, I'd recommend downloading JJ2+ and checking out levels like Rocket Powered Rabbits or Ozymandius.