This option was hidden as part of an effort to simplify the user interface. However, the query used for detecting custom field with values for issues of the exported projects can be heavy on a large database. Actually in some cases this query completely stalls the export. The exact reasons are unknown, but they could be related to database lock issues or poor DB performance. See for more details PCSUP-10 (or possibly PCSUP-26).
The idea is to put this option back in the user interface, so that in those cases the user has an option that keeps filtering custom fields without running the said query.