Mail.app: How can I archive the "smarts" of Smart Mailboxes?
Well, really, a smartmailbox is like a rule that is stored inside a mailbox.


I would suggest, creating the criteria for a smart mailbox as a real rule. 
Mail(menu)>Preferences>Rules(tab).
This way, you can just check/uncheck those rules when you want. This may adversely affect the rest of your organizational routines. However, you can choose to move or copy the messages, so perhaps copying could avoid the aforementioned caveat. Or an alternative
is
For me, if I go (in Finder) to /Users/myusername/Library/Mail/V2/MailData  there is a file called SmartMailboxes.plist . You could always drag this out (Mail should not be running), and return it when you need it again.

(There are also these associated files:


SmartMailboxes.plist.backup
SmartMailboxesLocalProperties.plist
SyncedSmartMailboxes.plist
SyncedSmartMailboxesLocalProperties.plist
VersionedSmartMailboxes.plist
VersionedSmartMailboxes.plist.backup
that may either need to be moved with, or just deleted. I don't use smart mailboxes at all, just a few dozen rules that I have changed/deleted/had in various forms for years over multiple OS/computer combos.) (Italics indicate a file that is there if you have synced smart mailboxes, which I never have, so that file doesn't exist for me, but does for the OP).

as far as a terminal shell script, you would want to edit the relevant plist files with the strings you need, by adding/removing them as need. You will get the strings you need by looking at the files themselves. You might want an app to look at them cleanly though, this could be XCode, PlistEditor, or something lite like TextWrangler if you're not messing around with XCode.


Notes: I'm running Mountain Lion with Mail.app 6.2. You should endeavor to always give the software version number of all relevant apps/os's to help the helpers help. I don't know if those files exist in the same way for you (more/less/different name/location), but the place to start for any recent Mac OS X version is the ~/Library/Mail (where ~ is your username/home folder), if your library folder is invisible you can get there by typing in the string in the window that pops-up with command-shift-g.