Currently yes. We blank it out in the update progress output, but it will get stored into the checkpoint if used directly as an input to a resource, and so will be visible in contexts where you see the checkpoint file. We're considering options for a first-class notion of Secret value that can flow through a program and be encrypted even in locations it gets serialized (checkpoints or runtime functions). See
https://github.com/pulumi/pulumi/issues/397.
We also added this to our FAQ recently - see
https://pulumi.io/reference/faq.html#are-my-secrets-ever-visible.