The conversion of PDF documents (both using pdftotext or TextLightning) to text may fail - there are often no such things as words or strings in PDF documents and therefore those utilities have to rebuild the text. And this does not always succeed.
I like Index import very much, but the "index" will be blank (hence, unseachable) if the PDF file is image-only, or is encrypted. To check the success of an Index import, open Info for the new file. "Kind" should display "PDF + text" if successful.
If a PDF is image-only (contains no text) and you REALLY need to capture the text, it may be possible to run it through an OCR application, such as ReadIris 9.
If the PDF is encrypted, TextLightning version 3 may be able to capture the text. Or, if printing is allowed, print it as a PDF file from Preview – then try an import to DEVONthink.