Hi @nikma ,
By default on an MX all inter-VLAN traffic on the LAN ports is already allowed. So there's no need to create a rule. If you've previously added rules that block everything then you will need to create the rule you're asking about.
The MX is (generally) a stateful firewall, meaning that if you allow traffic in one direction, the return traffic will automatically be allowed back. So in this case you would write your rule as you stated and that's it. Return traffic is good to go.
As for why it's not working, can clients on the same VLAN as the NTP server sync their time? Is the inter-VLAN routing working correctly (i.e. can the client ping the NTP server?)