If you know your instance takes long to build, you should set the health check grace period. https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGui...
Or if the checked service comes up before the system is ready, set a cooldown on the scaling up https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGui...
Or in extreme cases, prepare a complete AMI to boot from. This is not a NixOS issue. This it completely on how you operate your AWS.