For migrating data, I have always used rsync in the unix world. Even very large filesystems give a very quick final sync. Seems to me that there are several rsync ports to windows - you might try one of these to see if you get better performance.
As for importing the shares, I think you're stuck doing it manually. If there was a way to export the existing shares into a text file, there would be a pretty good chance you'd be able to manipulate the data into the ONTAP commands for creating the shares - but I'd have to see it....
Radek, the OP is migrating from windows to NetApp, so there is no cifsconfig_shares file to copy.
In addition to the cifsconfig_share file (just in case someone else trying to migrate shares from NetApp to NetApp reads this), there is some share information kept in the registry. Look for "options.cifsinternal.share" in the /etc/registry. Only some options are here (umask stuff, at least) - there may be no entry for some shares.