Is there a time sync process on the Docker for AWS nodes?

You can verify resources that are created by cloud formation Docker-no-vpc.tmpl from the link you provided.

Second thing, do you think ntpd have something do with docker-swarm? or it should be installed on the underlying EC2 instance?

Do ssh to your ec2 instance and very the status of the service, normally all AWS AMI has ntpd installed.or you can just type to check

ntpd

If you did not find, you can install it for your self or you can run docker swarm with custom AMI.

UCP requires that the system clocks on all the machines in a UCP cluster be in sync or else it can start having issues checking the status of the different nodes in the cluster. To ensure that the clocks in a cluster are synced, you can use NTP to set each machine's clock.

First, on each machine in the cluster, install NTP. For example, to install NTP on an Ubuntu distribution, run:

sudo apt-get update && apt-get install ntp#On CentOS and RHEL, run:sudo yum install ntp

what-does-clock-skew-detected-mean

Last thing, do you really need the stack that is created by cloudformation?

EC2 instances + Auto Scaling groupsIAM profilesDynamoDB TablesSQS QueueVPC + subnets and security groupsELBCloudWatch Log Group

I know the cloudformation ease our life, but if you do not know the template (what resouces will be created) do not try to run the template, otherwise you will bear sweet cost at the of the month.

Also will suggest exploring AWS ECS and EKS, these are service that are sepcifly designed for docker container.