If you're not going to use TM at all, there is a hidden preference to turn off the nag, however it won't ever ask again, you'll have to either reverse the preference or set the disk manually via the TM Preference Pane
http://www.afp548.com/article.php?st...80109213724586
And if you're not a fan of terminal...
http://secrets.textdriven.com/
*the preference is listed under TM
As an aside, to my knowledge TM only asks this once per external disc and then records the dismissal (not sure where, possibly 'Volume/External Drive/.com.apple.timemachine.supported'?). Is it possible that SuperDuper is clearing the previously recorded dismissal when it clones the primary drive (which wouldn't have a dismissal b/c it's a system drive)