I just tried this myself in Webstorm, and get the same result in the Evernote web client--all color is stripped out, though at least the indentation is kept. I'm not in a position to test the fat client at the moment, but I'm betting it has broader acceptance of HTML formatting. I've dealt with rich text editors on the web quite a bit, and they're quirky. It's likely the Evernote web team had some issue and had to blacklist a lot of the tags.
That said, Evernote's formatting is becoming a larger issue for me. I write a lot of technical documentation, and code blocks are absolutely necessary for me. I'd be happiest if Evernote just decided to give developers the ability to use Markdown instead of HTML. That would solve a lot of issues by itself.
