There's not a single crisp answer to this question, but I can give you
the current status.
First, ctypes is currently used by the browser, so it is supported. The
JS shell defaults to having it off (and avoids an NSPR dependency with
it off), but SpiderMonkey is compiled with it enabled for browser builds.
However, I think people are trying to remove that usage. (I *think* it's
only used for an OS.File thing.)
I think that deprecation notice has been there for a long time, and is
mostly talking about how js-ctypes is nonstandard. Given that it's not
exposed to web content, nothing has really changed with respect to that
warning in a long time.
Additionally, and perhaps most relevant to you, people within the
SpiderMonkey team have been making noises about trying to get rid of it
entirely. I don't think anyone is actively planning on doing that
removal right now, and I'll get in the way somewhat because the static
rooting hazard analysis relies on it, but I'm sure I could come up with
some workaround to avoid that (eg by compiling my own shell with the
extensions I need instead of dynamically loading them; I control both
sides.)
So: for now, it's available and supported, but it's not safe to assume
that it'll be around for the long haul.