Is Ubuntu destroying my internal HDD?

TL;DR

No, Ubuntu is not destroying your HDD! :-)

The long answer:

HDDs die a slow, painful death like cancer, whereas SSDs just suddenly stop working like a heart attack : you can diagnose both by using SMART technology.

Why you heard the noises under Ubuntu and not under Windows is because Windows was installed first, so it resides on the inner side of your hard drive in the denser packed region, whereas Ubuntu was installed on the outer regions where the noises are more pronounced due to seeking.

And I can infer all this just from your description of the symptoms without having looked at your hard disk's partition table nor knowing how you installed your system...

What kind of sound does it make? If it's clicking you hear, then your OS MIGHT ACTUALLY BE DESTROYING YOUR HDD. The problem is ages old and involves Advanced Power Management feature parking/unparking the disk too aggressively. Try using hdparm to check the APM value (-B param). If it's less then 254, set it to 254 and check if it helps with the noise. If it does, make sure the value stays 254 at all times. One good way to ensure this under Linux is to use tlp. For the record, I've seen this problem occur in Windows as well with certain laptop models, but it's way more common in Linux.