I have not found any diaries, etc. that reflect the use of craters in Civil War entrenchments, although such use appears to have been very common and well documented in World War II
The reason that pits were not made from shell craters in the CW was due to the type of and size of artillery used. Except for seige operations, field guns used ammunition which unless solid, was designed to be exploded in the air above the soldiers. There were shells with concussion fuses but field artillery was too small and black powder too weak to leave the big craters that WWI and WWII high explosive artillery left. It is not uncommon to dig a CW ground burst and usually most of the fragments will be within a foot or two of each other. Not much exploding power in these type shells.
Bigger guns such as ship's guns or 100 & 200 lb parrott rifles could likely make a big crater if a shell dropped down with enough momentum to bury in the ground. There are not many areas where these types of shells were used against infantry but along the James River they were worrisom.
The CS section of the Howlett line adjoining the James River was inspected shortly after positions were established by the respective armies. I forgot what general did the inspection but the result was a significant strengthing of the line in areas where the Union gunboats or Federal river forts could shell the lines. The general was worried that a large artillery shell from these type guns could punch through field fortifications and would probably be capable of making a man size crater taking most of the breast work with it. Some of these strengthened lines are still surviving and are about 10 or 12 feet wide across the top of the works. (Parkers Battery by Krick)
Portsmouth Rifles, 9th Va. Inf.
CW show & tell.