Recall, too, that it is useful to watch a DEVONthink group (or Evernote notebook, Notes folder, etc.) if you anticipate that that source is going to change.
Is it likely that your hundreds of groups, and potentially multiple hundreds of annotation notes, are changing much or at all?
Instead of watching DEVONthink groups consider dragging those annotations to DEVONthink and then setting $AutoFetch=false for them. The annotations’ contents will not be updated. If the time comes when some annotations in DEVONthink are updated in that software then set AutoFetch=true for those notes, they will update in Tinderbox, and then you can set $AutoFetch=false and “de-couple” the Tinderbox notes from their DEVONthink source annotations.
This way you can get your annotations into Tinderbox for mapping, linking etc. – a very good use for Tinderbox, without being concerned about watching and the resources it might consume.
I also find it useful, in relation to this, to make Table of Contents documents in DEVONthink (see the DEVONthink manual) and dragging those into Tinderbox. The TOC document has a list of links to open in DEVONthink each of the documents listed in the TOC.