As far as the experience of last 2 days, here are the pros of using Obsidian or Diigo for bookmarks:
Obsidian Pros:
- Graph view is giving insight on big chunks of tags,
- Easy bulk edit using scripting since every bookmark is actually a flat files,
- Full text search and complex search using regex search,
- Open random bookmark (note) from time to time.
Diigo Pros:
- Easier to query by different means: tags, url, free text,
- Entry display is easier than files display in Obsidian,
- Easy capture new bookmark using browsers addon,
- Avoid duplicate.