I don't think they were trying to be funny. I think it's just jargon talk. I work with unicorns all day and this didn't strike me as an attempt at humour, more as a technical description of what is going on.

When storage availability is degraded and I can't even clone my repositories (not using the web interface at all) it is pretty enraging to see the status page and twitter account talking about angry unicorns. I get that ruby devs understand this, but not all of us who use Github know or care about them using Unicorn as their webserver. It seems to us like they are trying to be cute and funny at a poor time.

I agree. It's a perfectly cromulent description of the problem at hand.