Yes, they are. But only recently, and only a small relative about. I'd forgotten that they'd started doing it a couple months back. That's why I said 'basically all of them', because every other major site I'm aware of that accepts bitcoin doesn't hold any bitcoin. It's immediately converted to dollars at sale time because holding bitcoin for even part of a day is a huge and completely unnecessary risk for a retailer.
The timeframe I mentioned is relevant to Overstock because they were not holding any bitcoin last year. They only began accepting it this year and only began holding it more recently. So only its recent (poor) performance is relevant to Overstock and its investors. As such, it would appear to have been a bad decision in the short term.
I'm not the one in this back and forth who is cherry-picking. Bitcoin up over a different timeframe (a year, since inception, etc) is irrelevant to Overstock, just as its drop to 1/2 of its value over the last few months may be less relevant to your Bitcoin holdings.
Full disclosure: I hold .24826531 Bitcoin personally and in conjunction with my open source project and run Bitcoin Core 0.9.3 64-bit on Windows.