Nope, you can't do hashtags in CWs, and it's been closed as an issue, presumably as a wontfix:
@nangar I meant in the CW itself. I know you can search for hashtags within the content of the CW-hidden text.
@wohali OK, I misunderstood you.
@wohali And now that I understand what you're talking about, thanks for making me aware this issue.
@wohali Nope, you can search for hashtags hidden behind CWs. If you search for #nangartag, you'll get the test toot I made a few minutes ago to verify this.