I don't think greasing the splines on the flanges will do much for your clunk ; there are so many interrelated parts that contribute to the condition. IMO it's not a single source fix, you need to assess and address several driveline, control and suspension components.
You might however sparingly apply a thin coating (so it doesn't contaminate bearing grease) of moly paste to help minmize the splines from wearing further. I use a 60% moly paste for extreme pressure fittings like input shaft splines, and my axle flanges.
I had the same symptoms. Jacked up the front end and found that when I rotated the driver's side tire I had slop before the axle caught. Replaced both the axle and flange - sound gone.
Not saying that's your problem, just what mine was with the same symptoms.
Unlikely that it's the flanges. The splines are fine enough that if there were any play you wouldn't have a big enough gap to create an audible thud like the CVs or driveshaft.
It easy to check if hub flange to axle is your issue. Pull grease cap and look at teeth inbetween gap of C of snap ring, or remove snap ring to get a better view.
Loose wheel bearing and wide snap ring to hub flange gap set up a saw like action eating teeth.