Actually, the 36 gb drive would be faster for a server in most respects because it's a smaller partition field overall to traverse. Seek times increase access times on an exponential magnitude, particularly in a server environment where defragging is often a forgotten art and file systems largely resemble fine cheese.
If you're looking at a server environment for this drive, I'd recommend multiple smaller drives in a RAID array instead of a single large drive. Not only do you improve performance in many areas but you give yourself fault tolerance, a must-have in today's markets.