Samurai Jack - So...if that was the last remaining time portal in existence...then...what happened to this one?

You mean Aku would lie?! Who would think a villain might lie to the hero..

Perhaps Jack thought of the Guardian's portal as unattainable (since he didn't win the fight), and crossed it off the list of usable portals he could access.

However, it is possible that Aku discovered the portal and destroyed it himself. After all, Aku doesn't need to kill the Guardian. He just needs to blast the Portal, which is one giant-ass target for any single being to defend.