Does creating items in the Defense Factory help in defending your Supply Points from being seized?

Definitely yes. The number of defense facilities you have and their actual capability to defend you matters when it comes to protecting your base. As long as your defense line do not fall/break, you wont have to be bothered by being plundered. Other ways to fend off other attackers are:

1. Joining a strong Corps - security blanket from other attackers

2. using "Fake Army" item - renders your your base twice its actual power.

3. using Base Defense boost items - renders additional defense power to you for a limited time.

4. Increasing the level of Defense Line

5. Increasing your Army size on stand-by (ones that do not participate in resource gathering on the battlefield)

6. Using Aegis Shield

The only way is to make your officer stronger and take the supply seized back. Each time a victory will make the level of supply increase by 1. As the level increase the number, damage,hp of defense increase