If you delete a document it will be in the Trash for that database, or the Trash for the Global Inbox, if that is where it was before deletion. Click on the Trash icon in the sidebar to locate your deleted items. When you empty the Trash, the document is gone from DEVONthink, but will be in your computer’s Trash until you empty the OS X trash. When you delete OS X trash, it is gone forever. It is a good idea to keep backups of important files.
This is a very common topic here, and in the Literature and Latte forum. I would suggest reading the many threads that have preceded your question and then come back here if there is something unclear or specific to your writing. Lots of writers have spent a lot of time discussing using DEVONthink and Scrivener together – I encourage you to read these threads: