Unfortunately I don't have a clear way to reproduce this. It seems to happen randomly.
node:sqlite appears as a "Resolved Dependency", but all types are seen as "any", and no autocomplete.
Types appear to be seen for other node:* modules.
Tried disabled/enabling the extension, running deno clean, re-starting vscode.
Last time I got the types working I had a fresh install of Deno and re-initialization of the project. Types were lost again at some point during development