that sounds like a normal windows operation, on a old noisy hard disk, is it seagate or western digital?
lately toshiba has been very silent on my latest 3 assembled pcs and also very reliable
other than changing brand of hard disk, consider going for ssd only or a make a nas storage
encripting a hard disk on windows, well, the contents will be read by the system, because the system has the encription key, so it can rad the contents, only will not be readable by another pc, if you take out the hard disk and install it on the second pc without the right encription key
about the door of your house, don't paint it white, is a invitation for a graffiti