Its not possible to deselect 64bit definitions , its by design
it will download for 32bit and 64 bit definitions.
there are chances if definitions are corrupt these folders might grow, do a cleanup following this document.
Symantec Endpoint Protection Manager 11.x is not updating 32 or 64 bit virus definitions
https://www-secure.symantec.com/connect/forums/no-notifications-no-email-notifications
in your network if your not using network threat protection , then you can just download only antivirus and antispyware only
this feature can be set under
open sep manager
click on admin - sevesrs - right click local site -select properties
click liveupdate -keep the content revisions to 3
in the content types to download just select what is installed on your network, these settings should take care of the issue.
https://www-secure.symantec.com/connect/forums/sepm-unbelieveably-excessive-disk-usage