I have 2 Devonthink Pro databases I would like to compare to see what files are in one and not in the other. How do I do that? Can I merge them? If so, how? 
Simple merging can be done by exporting from one or more databases, then importing to another. Wise to have backups.
I can’t think of any easy, convenient ways to compare databases.
This could perhaps be done by exporting and then using FileMerge (which, I believe, must be installed as part of the developer tools from the DVDs–I could be wrong, I don’t remember).
I think you’re on the right track with the idea of comparing exported databases though it’s certainly not an easy or convenient method. 
Another possibility is to compare the listings created via Scripts > Export > Listing…
As I mentioned years ago, the output of Export > Listing… has been useless to me mostly because it’s not in a diff-friendly format. Someone wrote an alternative script that produced output with one document per line. I’m not sure it’s on the DEVONthink Scripts & Additions page; though it might be Shell Add-ons but that link to Eric’s site is broken.