It’s not about being anal and keeping things neat, it’s about recognising that you’re never going to reply to that email from 2 years ago, but it’s hiding that email you should respond to.
Be ruthless. Archive, delete in bulk. That sale 3 years ago is over, you’re never going to fix that NHibernate bug, and someone else is looking at it, it’s too late to sign the petition to bless the rain down in Africa.
And as I found when my phone broke, and I got thrown back to a version of Gmail without bundles, stop hiding things behind labels. If you’re not going to read it, unsubscribe or filter it into the bin. Lose the haystack, keep the needles.