What are the limitations of NTFS regarding the number of directories and max allowed files per directory?
Maximum allowed is pretty generous. Unlimited files in unlimited directories. The maximum files and directories on a VOLUME is limited to unsigned 32-bit minus 1 (4,294,967,295 objects). Practical limits are another thing, though.
Edit: 64-bit windows doesn't seem to change things. I can find no evidence that 64-bit servers have higher limits. The file limit is more of a file-system format problem than a kernel bit-width problem. The next version of Windows may allow more files, it doesn't look like Windows 2008 R2 will be changing this.