<p>Would NTFS allocation blocks of 16KB or 32KB make compile time faster in comparison to the default 4KB?</p>

I can't imagine that would make much of a difference - disk block size is pretty far removed from compile speed. With the amount of caching a modern OS does, it seems unlikely to be significant.
The real answer, of course, can be found by measuring it. Getting similar conditions between different machines with different disk block sizes might be tricky, though.