MongoDB / WiredTiger: reduce storage size after deleting properties from documents
Just to clarify, please be careful about using repairDatabase on a replica set node. repairDatabase is meant to be used to salvage readable data i.e. after a disk corruption, so it can remove unreadable data and let MongoDB start in the face of disk corruption.

If this node has an undetected disk corruption and you run repairDatabase on it, this could lead into that particular node having a different data content vs. the other node as a result of repairDatabase. Since MongoDB assumes all nodes in a replica set contains identical data, this could lead to crashes and hard to diagnose problems. Due to its nature, this issue could stay dormant for a long time, and suddenly manifest itself with a vengeance, seemingly without any apparent reason.

WiredTiger will eventually reuse the empty spaces with new data, and the periodic checkpointing that WiredTiger does could potentially release space to the OS without any intervention on your part.

If you really need to give space back to the OS, then an initial sync is the safest choice if you have a replica set. On a standalone, dump/restore will achieve the same result. Otherwise, compact is the safer choice vs. repairDatabase. Please backup your data before doing any of these, since in my opinion this would qualify as a major maintenance.