here is what I did. I created another tmp folder on which I am running the hazel scripts and once the proper tag is added to the file it moves the files to relevant folder which is indexed by Devonthink and the Smart Rule is immediately run.
it defeats the purpose that I have to manually add the file to indexed file.
I may need to optimize and run the same scripts with in smart rules and remove dependency on hazel or any other fodder action scripts.
for now it is resolved but need to optimize more on the workflow.