The Panama canal would have been wrecked by the passage of time as it is not just a trench dug between the two oceans. It relies on a lot of moving parts to facilitate travel of boats and would need a lot of staff even if there where still computers and power to run the locks.
That said I am finding I am not liking the later chapters of Dr. Stone. The pacing just feels a bit off for me while running a bit to fast for me to really relax into the story.