This article describes that in FortiOS version 5.2 Traffic Shaping was configured over firewall policy.
By default if traffic shaping wanted to be applied, It was just a matter of create a shaper and point it out on policy.
Now on 5.4 - 5.6 FortiOS versions there is no such option, It has to be configured using CLI every time it is needed to be configured inside the policy.
All FortiGate Version 5.4 / 5.6.
1) Go to Policy&Objects -> IPv4 Policy, select policy which Traffic Shaping will be configured and select 'Edit in CLI'.
2) Configure the following commands inside the policy:
set traffic-shaper <shaper name>
set reverse-traffic-shaper <shaper name>
3) Once configured, Traffic shaping configuration will be visible in policy by from GUI.
This steps has to be done on every policy to apply Traffic Shaping by policy.