I wouldn't exactly call it a problem. Every HDD is affected by it so you can't escape it (except by switching to SSDs). But yes, you can minimize its impact by buying a much larger drive than you need and leaving lots of free space. One of the tricks people did before SSDs was called short-stroking. You make a small partition for the OS first, then create a larger partition for data. This puts all OS files on the outermost tracks where the drive is fastest (hence the name - the read/write heads only have to travel a short stroke to reach the OS files). Data whose speed isn't as important ends up occupying the inner tracks.
I probably should've mentioned the effect of fragmentation is much bigger. Whereas writing data to the inner tracks will only yield about 50% of the max speed, fragmentation can drop the speed down below 1 MB/s (which on modern drives is less than 1% of max speed). It's why when you try to copy a bunch of small files (like MP3s) from one partition to another on the same drive, it usually proceeds at less than 10 MB/s. The drive is spending most of its time waiting for the read/write heads to move back and forth, instead of reading and writing data.
Incidentally, HD Tune is one of the better HDD benchmark programs which will measure transfer speeds across the entire surface of the drive, not just with a single file. In the resulting plot, you can see how the speed (blue line) drops to about half its max as you get to the inner tracks of the drive. And the seek times (yellow dots - time to move the read/write heads and wait for data to spin under the head) increases for the inner tracks (which are furthest from the read/write head rest position. The vertical spread of the dots reflects how long the drive has to wait for the data to spin under the head. The bottom is when the data arrives just as the head does. The top is when the head just misses the data, and has to wait a full platter rotation for the data to come around again.
http://www.hdtune.com/
I'm not sure how useful a HD Tune benchmark will be on a full drive like yours. But you can run it on a new drive to get an idea of the best and worst case performance you should expect as you fill up the drive.