Once the wort gets below boiling the isomerization process is really slowed down. This is why commercial breweries can add their whirlpool additions to 190F wort for an hour without gaining much bitterness. I've never used hop bags in the boil, but if you do, it's really up to you if you want to remove them, but not much more is going to happen once you begin to chill the beer down.
And yes, those things you see suspended over the kettle are hop bags. Most people agree that regular bags constrict the hops so they can't flow around the kettle as well, thus not being utilized as well, and the very large bags allow an easy way to filter out the hops, while maintaining good wort contact.