In response to the original post, the 2x500 may give you a slight read/write speed increase over the 1x1000 because they will have less space to search through, but we're talking milliseconds here... If you do 2x500 and do RAID 1 I believe it is, then you'd be able to have 1 fail and still have an exact duplicate of it, however, you'd also be losing 500 GB of space. Personally, I like to have smaller drives that way if and when one dies or is in the process of failing, you can make it easier to save or transfer the data to free space on one of the properly functioning drives.
To answer your question kookoo, I don't believe the difference would really matter, since the processor would have to deal with each program in turn. If you think of it like this, the terminal can only handle one processing line at a time, so just adding another line for the data to come from won't increase the boots times. In fact if my understanding is correct, you'll probably make it slower because the computer will have to switch between the two different sources instead of just being able to concentrate and dedicate itself to one source.