The Dump is a flaw in the story. If all the capsules came from the Pearl, then the Pearl would have to have a storage room at least as big as the Dump that was full of empty capsules. Logically and logistically, the DHARMA Initiative would have only required a few capsules. Each time a capsule was sent, its contents would be emptied and returned to the appropriate hatch. The Dharma Initiative would have only required a few capsules for each station, not the thousands shown at the Capsule Dump.
Hugh Mcintyre said on "Jimmy Kimmel Live" that the Dharma Initiative ended in 1987. After the initiative lost funding (or was ended) they stopped collecting the notebooks, hence the pile of notebooks that are left today.
DHARMA did not plan to study the logbooks, but if something went wrong the logbooks would be collected and studied to ascertain what went wrong.
The Pearl was the real experiment, not the other stations. DHARMA was testing the people that were working in the The Pearl by watching how much they would write about the people on The Swan and other stations. The test subjects probally never stopped before The Purge.
Regarding the positioning of the capsules
Notice in the location image provided that the capsules are not logically positioned based on the position of the pneumatic tube. If they were released from the tube, the highest point would be below the tube in a mountain shape. Various hills and valleys of capsule piles would not exist.
The shape of the pile is simply an oversight on the part of the set designer or matte painter.
The pneumatic tube dispenser moves around, which explains the various pile tops (though not likely due to the tube being fixed to a concrete pad in the ground).
Someone or something ensures the capsules are moved over from the dispenser in a timely fashion.
Weather conditions adjusted the shape of the capsule piles.
The tubes come out with extreme force and bounce several times before coming to a rest, creating this modified bell curve pattern on the grass.
The slope of the ground has avoided the formation of a big capsule pile just under the pneumatic tube.
The capsules were moved by the "earthquake" that happened when Desmond was late entering the numbers (and also brought down Flight 815).
The air pressure in the tube is inconsistent, so that tubes are shot out at varying velocities. Since the island seems to draw electric power geothermally, local changes in weather patterns/tectonic shift could affect how much power the motors receive - especially if they weren't constantly maintained.
The Others or the leftovers of the Dharma Initiative regularly read the notebooks and (sloppily) sort the capsules into piles, possibly based on which station they come from.
Miscellaneous
Either all of the notebooks and papers were brand new to the Capsule Dump site when Jack, Kate, and Sawyer find it, or its protected from the rain (and wind and other elements), otherwise the notebooks would have been damaged.
There is an element of time travel involved. When Kate reads from the notebook, she says "subject moves the ping pong table." Later on in the episode we see Desmond move the ping pong table when looking for the book with the key in it.
The dump, like The Door, is a mock up. It was put together by the Others to distract, confuse, or mislead the survivors.
Is the dump referred to on the Blast Door Map. "Why so many DharmaTel relays in such an untenable location"?
The workers in the Pearl Station recorded what was done in the Swan station so that The Hanso Foundation would know what exactly what was done to change the Valenzetti Equation
A possible explanation of the Pearl Station needing a storage area for all the capsules is that there is a storage area elsewhere on the island that sends empty capsules pneumatically to the Pearl.
A DHARMA van would normally be parked under the pipe mouth to collect them and then bring them back to the Barracks for study (no DHARMA vans are available following the Purge)
