I have been using these three items for the past 3 months or so and have had a lot of enquiries as to which is best. The short answer is none of them, they all have their pluses and minuses depending on what you need.
The Hyperdeck wins hands down, approx £300, $350, an extra £75, $100 for a mounting plate.
The Ninja is £800, $1000, the Samurai £1000, $1200. None of these prices convert properly, the prices are simply higher in Britain.
They are equally well built, the Hyperdeck could be used as a weapon, especially with the mounting plate. The Ninja and Samurai both come with a fitted, very well made Pelican style case. As a package the Ninja edges ahead.
Until a few weeks ago the Ninja/Samurai scored heavily by having Apple ProRes as a codec, whilst the compressed option from the Hyperdeck was limited to Avid DNxHD. Now they compete on level ground and as a ProRes user the Hyperdeck became instantly more useful.
The Ninja/Samurai have external Batteries which can be hot swapped, this is much more flexible than the Hyperdeck with its inbuilt battery. Longer shoots need access to mains power or some form of external battery backup.
Where the Blackmagic unit scores is its option of HDMI or SDI. The reason that Atmos offer two options is that the Ninja has HDMI and the Samurai SDI. I often do 2 or 3 camera shoots so having 3 units is no disadvantage. Atmos do offer add on converters HDMI to SDI and vice versa, but at a couple of hundred £ or $ extra soon adds to the cost.
The Ninja/Samurai on their side score by having a touch screen, which controls all functions including formatting of media and doubles as a Monitor, albeit not Hi Res. I find the Samurai Monitor particularly handy with my Canon XL H1 which has had its useful life extended by tacking on a Samurai. I was using the Focus Unit specially built for the XL H1, but unfortunately a change in Quicktime which is not supported by the new owners of Focus have made the unit all but redundant.
The XL H1 is a terrific Camera (although bulky) and it is nice to get an extended life from an old faithful. It also has the advantage of automatic Backup i.e. Tape.
The Hyperdeck has mainly been used with a Sony EX1, quality great, hassly trying to fit the Camera to the Hyperdeck. The mounting plate is not much good unless it is being used to attach the Hyperdeck to some form of external rig, so I have ended up stringing it to an external Manfrotto Arm when the camera is tripod mounted. In fairness the Sony is not ergonomically good when handheld so I do treat it as a Tripod Mount Camera.
Another area where the Ninja scores is it can use SSD's or Mechanical Hard Drives, so whilst SSD's are too expensive to use for an Archive (unless you are the BBC) it is possible to buy small Mechanical Drives for little more than Tape used to cost. Having said that the reliability of SSD's is greater and I have hardly used anything else. The SSD's can be formatted in the Ninja or Samurai unit, the formatting and indeed choice of Codec for the Blackmagic unit needs to made using a utility Desktop or Laptop programme. This might be inconvenient to anyone who wants to switch Codecs during a shoot, although I can't think why they would.
For me I can see no difference between the Atmos and Blackmagic units in ProRes which is what I use. The Blackmagic unit can also record 10bit Uncompressed so for anyone who needs the ultimate in quality the choice is made. Having made that point I am unlikely to ever use uncompressed because of the massive overhead both in space and processing power required. As mentioned the Blackmagic unit records to ProRes and Avid as does the Samurai, at present the Ninja 2 is ProRes only.
Either option is excellent and both options represent superb value, so far they have all been reliable in field conditions and the only complaint about the Hyperdeck is mountability and battery options. The Atmos units have performed flawlessly and incidentally use Sony Batteries which can be bought for a few pounds from Amazon. If Blackmagic address the "where to put it" (no rude remarks please) issue and some sort of external power (apart from a very long cable) and keep close to the current price they will be on a par with Atmos, meantime the Ninja and particularly the Samurai with its slightly larger screen just take the trophy.