No, you don't have to clear the entire boatyard.
Sometimes, the cards in between stages of a boatyard instance can give out unbound items, such as Gulu shield, Shako, etc.
However, if you clear a boatyard instance, you'll be able to flip 2 cards in the end, so you'll have a better chance in getting unbound items.
Also, if you send a private message and expect the person to reply you, please allow everyone to send private message.
How to enable private message from people:
1. Hover your username on top of the screen.
2. Choose Setting.
3. Click the tab saying Privacy and allow anyone to send private message as shown on the figure below.