My 12 year son has a fire 8HD tablet attached to my amazon account. My wife's kindle is attached to her amazon account, which is in our "family library". I have a kindle as well.
The books app on my son's Fire shows all the kindle book covers we have purchased on our two kindles - the books themselves are not downloaded to the Fire.
How do i hide the book covers without losing them from the two other kindles?
You can't unless you have your son added to your family library as a child in which case you csn select what he sees. if he is just on the main account he can see everything that is in the Amazon cloud which you have bought.