Q: Slow hard disk

Hi,

Make sure OS X is up to date.

Open System Preferences > App Store then click Check Now.

In theory your disk could be generating silent retires as it struggles to read data on marginal sectors.  Assuming we are talking about the

MacBook Pro (13-inch Mid 2012), iOS 9.3.2, Very slowly hard disk maybe bad sec

you listed in your post, that disk would be 4'ish years old.  That is in the zone of maybe going bad.  The problem is that some disks last longer, some go sooner.  There is no way in the forums to actually tell, so this is just a guess.

You could make a Genius Bar appointment at your nearest Apple Store and have them run their extra strength diagnostics that might turn up something.

It is also possible that over the years you have accumulated other misc 3rd party utilities that are now sucking he life out of your system and should maybe be removed.  You could post the EtreCheck output and someone will take a look and give suggestions.

If it's still possible, open Console.app (Applications/Utilities) All Messages and enter "I/O" (no quotes) in the search field. If the drive is becoming toast, you will see an I/O (input/output) error of some kind. This is usually fatal.

Do a backup, preferably 2 backups on 2 separate drives.