here is a hypothetical situation to represent the craftymynes server:
a perfect world where no surrounding chunks have to be loaded, on a single block an item is spawned every minute
after 5 minutes, 5 items will have spawned. this is the max amount of items this contained system allows for, this is its equilibrium point
let's say every 15 minutes all items magically disappear, hooray!
except, in exactly 5 minutes, the world will be back to 5 items, and equilibrium will be achieved again
it is safe to say that in this system, the clear would be negligible to the performance of the server, especially since the equilibrium point will have been reached relatively fast after the item clear. this is most likely what happens on craftymynes, just with a lot more items, and a slower item clear (items still despawn after 5 minutes)