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The size of your data center and the number of servers justifies an uncompromising design. Computer Room Air Conditioners (CRACs) are precisely what the name implies: air conditioners designed specifically for the needs and demands of the computer room. I'm assuming from the wording of your question that the roof-mounted Air Handling Units (AHUs) that you are also considering are conventional units designed for the standard office environment, and probably run off the building central system. A data center should be as independent as possible.
It is unlikely that standard rooftop AHUs will maintain the close tolerance temperature and humidity control you should have in a high-availability data center environment, which it appears you intend to have if you are staffing the NOC 24x7. (Incidentally, the NOC should be provided with a normal office environment to make it more comfortable and controllable for the occupants.) Standard AHUs are normally designed to handle more latent heat (evaporation of moisture from human activity), whereas CRACs are designed to humidify while also handling mostly sensible heat (the dry heat you feel or sense coming off of computer hardware).
You don't identify where in the country you are located, but if you are in the North, roof-mounted AHUs can present some operational and maintenance problems in deep winter, and if you're in the South, they may not provide the level of humidity control you need. With today's concerns about energy efficiency, you will probably also find CRACs to be more economical in the long run, particularly if you are in a part of the country where you can take advantage of winter temperatures to utilize "free cooling."
The raised floor question is one that is widely debated these days. I still prefer a raised floor in most situations, particularly if I have enough building height to utilize the floor for air delivery. (That means 18-inches minimum, and preferably 24-30 inches. It also means controlling obstructions under the floor, including piping, power and cable.) With roof-mounted AHUs, you're not going to deliver the air to the floor, so it becomes a matter of personal preference and budget. I still like to have power and permanent cable infrastructure under the floor if I can, but others have different opinions.
If you can't make a raised floor high enough to use it for efficient air delivery, then, whether you use roof-mounted AHUs or CRACs, you will be delivering air from overhead. This can certainly be done, and can be done well, but it requires more design than simply blowing cold air into the room. Warm air rises, so dumping cold air in from above in the closely-coupled "Hot Aisle/Cold Aisle" design of a data center essentially contradicts the laws of physics since the warm air will rise and mix with the cold. Either solution will require well-designed ducting to cool and operate efficiently. Therefore, this is probably easier to do, and certainly less space consuming, with roof-mounted AHUs for which the return is already at the ceiling. On "Top Blow" CRACs the return air intake is at the lower front or back of the unit, which presents greater duct design problems. In my opinion, however, unless other factors preclude it, I would opt for CRACs in an important facility every time.
If I'm interpreting your question correctly, you are asking if you should use enclosures with fans mounted on the rear doors, blowing into the hot aisles. I consider most of the "fan boosted" solutions to be means of addressing problems caused by a poor basic cooling design. I say "most" because there are cabinets that are truly engineered to support higher density loads than can be achieved with high-flow cabinet doors alone, even in a well designed facility. But these cabinets generally duct the hot air to an isolated return path – usually a plenum ceiling – so they are solving more than just an air flow problem; they are also preventing re-circulation of hot air, which in itself makes a big difference. Remember, however, that fans will try to pull air out of the floor or cold aisle in the quantity they were designed for, and this may air-starve other equipment farther down the row. (Variable speed fan control helps, but if heat load is high the fans will still try to pull maximum air.) A data center is a complete "system," and you can't just insert a "solution" into the middle of it without affecting things elsewhere. There is simply no "magic bullet" for the problem of high-density cooling.
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