Would using seafood stock instead of chicken broth/stock work in a butternut squash soup?
TL; DR

As long as you get the balance right anything that's tasty separately can be mixed together and still be tasty.

What I would do is to make the butternut squash soup first without any stock, set aside one bowl of said soup and then little by little add the shrimp/lobster stock into the kettle until just right to your taste-buds.  Then add the separate bowl back into the kettle.

Why? Your taste-buds will have gotten gradually used to the shrimp/lobster stock and the final product will be slightly over the top, so adding the bowl back in will make it just right for your guests.