Good point of discussion
There are two reasons why I choose to use bookmarks rather than indexing my vault(s):
(1) I use Groups in Devonthink to keep multiple sources of information on a given topic - Word files, PDFs, URL links to websites, links to pertinent Google Docs or Google Sheets, Aeon Timeline files, etc etc. All of these can be viewed while in Devonthink by simply right-clicking and choosing “Open With” for files or simply double-clicking for bookmarks. Now that Obsidian has a URL scheme, I can use Obsidian as another type of information to associate with a group and I can open an Obsidian Vault by simply double-clicking the bookmark while inside Devonthink.
If I were to index Obsidian vaults, this would not work. Obsidian files are Markdown files of course, but it is not possible to designate Obsidian as a recognized MacOs app for opening Markdown files. So if I were to use indexing, I would have to open the Obsidian files some other way outside of Devonthink. That would make the workflow slower and much more inconvenient.
(2) In general, I prefer to avoid indexing with Devonthink whenever possible. There are a variety of “gotcha” situations which can occur especially when trying to copy or duplicate or replicate indexed files. I think long-term the data is more secure either (a) Imported into Devonthink [not possible with Obsidian] or (b) Kept with its native app and then bookmarked with the URL scheme.