First the title of this thread is incorrectly name "driveshaft clunk". This thread actually deals primarily with the propeller shaft cluck of slide yoke.
So, safe to say, if you (I) have D-N-R clunk as well as getting on/off gas at speed clunk ... it's likely a multitude of things that need attention?
Yes, which is usually the case with our ageing fleet.
Number one under-maintain area I work on, is front wheel bearings. Neglecting them cause more expensive repairs of the front drive shafts yielding D-N-R clunk. What happens is the hub flange spline/teeth wear out needlessly. Also the axle of front drive shaft splines/teeth wear out needlessly. Wheel bearing require servicing every 30K miles. This is either done improperly or not at all in every 100 series I've seen.
Good used axle of front drive shaft
Hub flange, about to fail.
New hub flange.
Propeller shaft clunk:
If slide yokes neglected it may wear out the splines of the slide yoke of propeller shafts. Then you'll chase the clunk with frequent lubes of slide yokes.
So often someone buy a 20 years series 100 w/100, 200 or K miles. They see the service history is great and they just drive. They'll be unaware that Toyota puts out a maintenance schedule. That ever 5K miles something needs servicing, which is mostly fluids/lubes.
I just inspected a very highly serviced 06LC w/200K. With 40 plus service events at one Toyota Dealership over the years. Service history shows Lube, Oil & filter every 5K miles, great right! Yet above the spiders and propeller shafts slide yokes, it's as dry as the Sahara. No old built up grease on undercarriage, from being slug above the 6 grease zerks. Now, unless someone took the time to clean all the old grease as it came out of the spiders (AKA, U-joints) and sliders yoke each lubing, it obviously has not be lubed.
All rubber gets old and dry, in need of refreshing. This includes engine & brake hoses and suspension bushings.
Front drive shaft CV bearings do wear out. They'll click mostly in turns.
Inspect, inspect, inspect.
There is a wealth of information in "MUD". So much you can diagnose and fix any issue that may come up. The trick is to get the rig's maintenance up to date. Then enjoy, for a million miles!
Once these are base line, bring back to factory spec. They don't clunk and are a please to drive. Keep maintained, and they're reliable and can run on the road or trail as long as you do the up keep.