Is repeatedly reading a drive harmful?
This is likely a hard drive power management and sleep issue rather than an issue with the drive. When unused for a few minutes, the drive goes to sleep, possibly making a noise while parking the heads for safety. Your script accessing it in shorter intervals prevents it from going to sleep. You can confirm if this is the issue by observing how long it takes to access something on the drive after it makes the sound (and goes to sleep). If it seems slower than usual, it's because of waking up from sleep.

Firstly, you should confirm if OS X is making the drive sleep and/or if the drive's firmware is the culprit:


Disable your script.
Go to System Preferences > Energy Saver and see if Put the hard disk(s) to sleep when possible is enabled. If it is, disable it and observe the behavior of the drive.
If the OS X configuration doesn't help, check the drive's make and model and see how you can disable sleep from the manufacturer's support site.


On one hand, disabling the sleep behavior would increase the amount of power consumed (even if it seems insignificant). On the other hand, if you would be using the drive somewhat often while leaving it connected permanently, it may be a good idea to just having it running and avoid the lag of a sleep/wake cycle.