I’ve posted about this before. I was advised to uncheck the decluttering option, and to wait for the next maintenance update. I’ve done both, and increasingly the problem is getting worse. The only way I can read pdfs in DT is to open them in the original application.
So the PDFs can be displayed in other applications but not in DEVONthink? This is a random issue of Sierra’s PDFkit, you could either upgrade to High Sierra (recommended) or enable a workaround (see hidden preferences in help).