"Youth," by Joseph Conrad, was originally published in 1898 and the more famous publication came later in 1902. The story, which is told as a flashback, occurs twenty-two years prior to the telling, so it would be set in 1876, if we take the date-of-writing as the date of telling. However, there is no indication in the story of when it is set; while the story is semi-autobiographical, Conrad may easily have intended it to be set before the 1869 opening of the Suez Canal.
Another strong possibility is that the Judea, the ship in the story, was simply too large to navigate the Suez; at the time of its opening, it was only 26 feet deep, and while the Judea was under-weight empty, it might have had a very deep draft after loading cargo. Too deep a draft would preclude the use of a shortcut.
Finally, at the time, sailing around Africa to reach Japan was a known and normal journey; many traditionalist sailors refuse to take an unknown voyage or sail via a new waterway for superstitious reasons. In any event, the Suez Canal is not mentioned, and it can be safely assumed that Conrad was more concerned with the adventurous nature of the tale than expediency. Remember, if the trip is short and safe, there is no story.
Thank you. I found out that because of the prevailing winds, Mediterranean east to west, sailing ships could not sail down the Suez Canal. It was not until 1878 that the first sailing ship was towed down the Suez. It was not a normal thing from the beginning. But the answer was to be found in Suez history and thus was not a mistake on Conrad's part, especially since the Palestine barque did not do it.