If, for any reason, you need to use the L1 construct I found this documentation to be helpful:

https://docs.aws.amazon.com/cdk/api/v2/docs/aws-cdk-lib.aws_ec2.CfnLaunchTemplate.html

The reported example is a bit annoying but I tested it and it works:

declare const cluster: eks.Cluster;

const userData = `MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="==MYBOUNDARY=="

--==MYBOUNDARY==
Content-Type: text/x-shellscript; charset="us-ascii"

#!/bin/bash
echo "Running custom user data script"

--==MYBOUNDARY==--\\
`;
const lt = new ec2.CfnLaunchTemplate(this, 'LaunchTemplate', {
  launchTemplateData: {
    instanceType: 't3.small',
    userData: Fn.base64(userData),
  },
});

cluster.addNodegroupCapacity('extra-ng', {
  launchTemplateSpec: {
    id: lt.ref,
    version: lt.attrLatestVersionNumber,
  },
});