What about the DC-9's wing makes wingletting it so difficult?
I do not know, and I have looked for answers for a little bit. Interesting question. I have seen it said that the DC-9 has a high aspect ratio, which may be a factor -- resisting a wing-axial torque is easier with a longer chord, which all things being equal, would be a lower aspect ratio.  Still, a split winglet (part up, part down) or tip fence like on the A320 could mitigate that particular torque. Ground clearance comes into play then, with the low wing and very low dihedral.  

So, my other suspicion is that resistance to flutter might be an issue -- podded engines (podded correctly) combat flutter. Rear-mounted engines do not. If the winglet tended to induce flutter, it might be tougher to suppress. Nobody wants to re-engineer the spar box for the scanty gain offered.