JD_Toims - 8:21 pm on Nov 5, 2013 (gmt 0)
Well, let's see -- It really boils down to two options:
1.) Google's lying when they say 404s don't hurt, unless you have links to them, which means somehow, some way there's a benefit to Google to not simply let webmasters know they should not have 404s errors on their site, otherwise there would be no reason for them to lie about them having an impact.
2.) You had legacy pages "go missing" for 3 weeks, possibly (through non-dynamic [in-post]) links to those pages, plus you lost all inbound link weight, trust, freshness and everything else that passes through links until you fixed the hack, the legacy pages were "found" by your server, and Google respidered the site.
Personally, I'll go with Option 2, because 1 makes no sense to me. Plus you lost every ranking factor that passes through inbound links, I have yet to see anyone *prove* it was the 404 errors that were actually the issue, and I've taken a site with 1000s of 404 errors reported in WMT from 1 page indexed and 0 traffic to 12,000+ pages ranking in a competitive niche without ever looking at a WMT report, fixing, or "clearing" 404 warnings in WMT.