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-s is short for --string. It expects, quote, “a string provided as an _argument_” [emphasis added]. So << EOT is consumed by the shell. The _shell_ redirects the heredoc as stdin to the process. Consequently, it's plausible that eyaml(1) complains.

You probably wanted to do something like:

eyaml encrypt --stdin << EOT

Anyways, why do you care about encrypting a _certificate_? Isn't it a _public_ certificate you're trying to encrypt?