All the information about Pokémon, items, enemy trainers and so on are written in the PBS files (the .txt files in the folder "PBS"). RMXP's Database simply cannot record the information we need, which is why the Database isn't used (except for tilesets). Have a look through the PBS files, and through the wiki (link in my signature), to find out more.
There are a lot of special features in Essentials which apply specifically to Pokémon games. That's why there are a lot of scripts. Fortunately, you won't need to worry about them unless you're doing something complicated. It's perfectly possible to create a Pokémon game with Essentials without ever looking at the scripts.