A palette in Mathematica is just a notebook. So one could write a little function that closes all the palettes that are open, use Hook and then reopen what was closed. I don’t really use palettes, so I don’t have a complete solution, but as an example, to close the basic math assistant palette one could do:
Notebooks by itself gets a list of all open notebooks (and hovering over the resulting objects will provide the path needed to close them).
Not super elegant, but if you have the same set of palettes open this might be an easy way of quickly closing them for Hook to operate and then opening them back up.