You do it because it is often required by law when abandoned. You don't want anyone falling by accident if the lid gives way.
Normally you fill them stone, sand or clean fill.
Normally you fill them stone, sand or clean fill.
You say you're covering it with a deck? It's possible that one or more of the posts will need to be cemented into the ground right where the cistern is now.So, assuming that safety and code requirements are not an issue, can you think of any reasons to get rid of it?