A very big difference, yes.
mktNoTrack = do not rewrite links to bounce off the click tracking server (branding domain) before redirecting to the target. Used when you specifically don't want to track Clicked Link in Email events in the Mkto database, or you need to have to widest possible penetration (i.e. to devices without JavaScript) and are willing to accept not tracking clicks.
mktNoTok = do not add the _mkt_tok parameter to the target link. Used when the target link does not behave properly -- for example a mailto: link that should not have extraneous URL info or a static file that won't download when there are query params -- or when you specifically do not want web page views to be associated with the lead.