Yes, especially if you want to synchronize with other devices, regardless of the method. But also if you use Joplin without Sync.

For example, what about foreign keys?
Resources, tags refer to notes that no longer exist. What happens if a tag is opened in the GUI that refers to notes that no longer exist because they have been deleted directly from the database? I don't know, Everything can be ok, Joplin can behave strangely or crash etc...