I have a loud, deep sounding knock seemingly coming from lower half of engine. I've been pricing rebuild kits in order to weigh my options. The kits don't mention piston rods. Am I missing something?

 

Rods are not included in kits. Unless bent or damaged, the rod bearings are changed.

If a rod bearing the crank journal may now be damaged from pounding, you need to inspect for this.

If you do rebuild check the following:

Engine has an issue with the oil drain holes in the piston oil ring grove plugging up, the result being excess oil consumption. The Toyota fix is new pistons.

Certain head bolt block bolt threads may pull out due to a design issue. The fix is to install threaded inserts for these holes.

The above issues are well known and can be found by an internet search plus threads at this site and others.

It is typically cheaper to buy a used engine.