After Sierra update, a new bug was found where ssh-agent no longer remembers the passphrase for keys added. Not surprised by their answer, Apple stated TL;DR: is not a bug, but a feature.
Many threads I've read revolves around using ssh-agent -A/-K but the problem is not the loading, but that I never wrote my passphrase down anywhere.
What do I do now? Can I retrieve my passphrase from Keychain?
PD: The reason I don't know my passphrase is the whole point of the setup was not to write down a passphrase but let keychain manage it in order to centralize passwords, as I followed some best practiced (I think it was GitHub's?) where they mentioned "using easy to remember passphrases are easy to crack; using random letters/number/symbols are hard to remember so you most likely will write it down, which is also insecure. The solution is letting keychain manage it" or something like that.