Good questions. If I create a link in an HTML document with something like `x-devonthink-item://276FA79C-08F1-4E3B-9767-0E0E427F6498` as the URL (href), both Safari and Firefox (Mac) ask if it's ok to open the link in DEVONthink, and then will do so if I say "Allow" or "Open Link" respectively.
If I create a link using the same URL in a TiddlyWiki document, clicking the link just opens the "Missing tiddler" tiddler. I've tried in Firefox, Safari, TiddlyDesktop and Node versions.
My hunch is that TW intercepts links so it can handle them however it needs to, and doesn't recognize the "x-devonthink-item" as a protocol.