If we're using a plugin like minervaSEO or communitySEO on our forums right now, will our SEO be completely shot to hell once we upgrade to IPB 3.0 and start using the new built-in features?

in short, yes. Someone might update it to plug into the ipb system like the tagging feature those mods use which isn't included in ipb3's seo.

No, it shouldn't have a huge effect, assuming that you correctly redirect the old URLs to the new ones.