Actually unless the system does a lot of swapping (in which case SeZo is right) I doubt if HDD orientation will make a major difference .. effectively this is only going to have to keep up with an ethernet link.
(theoretically what SeZo says does make sense though)
Putting the CD-ROM at the end would also make it easier to replace it with a hdd at a later date for maximum storage without disrupting the rest of the setup.
That kinda makes sense
.. I thought Debian uses UUID's to identify partitions .. that said it would certainly make more sense to a human trying to make sense of it as we saw before