They should be fine but I would leave CS3 installed just in case. With more complex documents you may be better off making small changes in CS3 and you may also want to export to INX and open that in CS6 to force all the text into the new text engine for documents that will be thoroughly updated.
Can they be opened directly? Yes.
Should they be? Harder to answer.
I've never had a problem with any file I created moving from an old to anew version, but we've seen reports here from other users who found converting CS3 or CS4 files to CS5 or CS5.5 seemed to be OK right up until they failed, often after extensive editing and while trying to export PDF. In general, exporting these same files from the earlier version as .inx or .idml, and opening that in the new version did not fail.
CS6 is too new to have had many similar reports, and I want to stress that these problems are probably isolated and indicate, I suspect, some underlying corruption in the original file (which might have caused failure in the original version at some point, too), but I've persaonally adopted a policy of export from the original for any file that is going to get converted. It isn't worth the risk compared to the short amount of time involved in taking precautions.