The point is to have spaces to put things, like optical drives, card readers, removable HDD caddies, fan controllers, tape drives, whatever have you. You don't -have- to fill them, but often you choose to fill at least one.
The more I look at it, the more I think "Well what else would they put there?". I mean, a standard ATX motherboard with a power supply above/below it takes up a decent amount of vertical space. You're as well having something potentially useful, like a 5.25 or 3.25 bay, rather than something not, like blank metal. There's no point for 90% of users to fill that space with HDD bays either.
i5-2500k @ 4.6ghz | ASUS P8Z68-V | nVidia GTX780 | 32gb DDR3| 2x SSDs 2x HDD | Antec Solo II
Alienware m17xr3 | i7-2630QM | ATi 7970m | SSD + HDD