As of [`40469d5`](https://github.com/flycheck/flycheck/commit/40469d58728a00cf0db18e487f1482c2a92245f0), Flycheck includes the warning code of ShellCheck in the messages, and provides a new option `flycheck-shellcheck-excluded-warnings` to exclude warnings from ShellCheck reports.

To suppress a ShellCheck warning for Flycheck, use the error list at `C-c ! l` to find out the corresponding error code (in square brackets at the end of the message), and add it to `flycheck-shellcheck-excluded-warnings`.

To globally suppress `SC2029`, add the following to your `init.el`:

    (setq-default flycheck-shellcheck-excluded-warnings '("SC2029"))

To suppress this type just for a specific file, type `M-x add-file-local-variable RET flycheck-shellcheck-excluded-warnings RET ("SC2029")`.

Note that these suppressions only work for Flycheck.  The message still appears if you run ShellCheck from the terminal, or as part of your CI or testing system.  To suppress a message for all instances of ShellCheck, as in [this answer](http://emacs.stackexchange.com/a/885/227).