Brass: Are shipyards "industries"?
It's just a mistake that the canal symbol is missing. If you look at the second edition rule book, you see the canal symbol on a level 1 shipyard:



The rules also say


  If you have just completed the Canal Period then remove all canal 
  and Tech level 1 Industry counters, along with any cubes on them, 
  from the map.


No mention of the canal/rail road symbols. They a just reminders.

Since level 1 shipyards are also tech level 1 industries (they look and behave like the other industries and the shipyard counters are listed in the rules as industries counters), they are removed as well when the canal period is completed.

So the short answer is: yes.