Is there any disadvantage to selling a Bobblehead or a magazine in Fallout 4?
Solution 1:
You won't lose the bonus once you find them, but you will miss out on the awesome opportunity to display them in your home, also its way easier to keep track of which bobblehead you've found already if you still have them.
You can build a magazine rack (2 kinds actually) and bobblehead display station if you have the materials that are especially designed to hold those items.