Traditional APM estimated Nash as a strong positive in 2008 and 2010 playoffs. His RAPM chart (regular season with playoffs combined) shows him basically getting better every year.
It is possible that a playoff specific APM or RAPM for 2005-7 might look better for him than his playoff WS/48 for those years. But that data isn't publicly available at this time.
It is also possible that Win Shares' use of team average shot defense rather than just when actually on the court and / or counterpart data might have hurt Nash more from 2003-6 more than was appropriate.