I think that DT’s item links (x-devonthink-item://…) are more robust compared to regular file links (relative or absolute) since they’ll continue to function even if a file gets moved/renamed. IMHO, that‘s a big advantage.
In my view, the best option for you would be to:
- in your Markdown notes, use Markdown links with DT item links:
[link title](x-devonthink-item://…) - for each Markdown note, include the note‘s own DT item link in the note body itself, eg. like this:
---
ID: x-devonthink-item://…
---
That way, should you ever need to use your notes archive w/o DEVONthink, you can simply search for the item link‘s UUID. This would return the original note plus any notes that link to it. I.e., your link connections will still be valid. And this will work with any tool that supports search (even in the Finder).
Since your links consist of unique IDs, you could always transform your links into a new link formal (like e.g. [[link ID]]), using a simple batch search & replace action. With a small script, you could also transform your entire notes archive to use date-based IDs instead.
So IMO using DT‘s item links together with item links in the body of the note gives you stable links that provide enough options to reuse or transform your notes archive if necessary.