I've run into grapple connections that become unselectable too. It's super rare so I've yet to find the cause. If you find any way to recreate that bug please let me know because then it's easy to fix.
Water is going to have a quality setting in the video options panel. On the lowest setting you will be able to disable it's dynamic surface, and then the performance hit is negligible.
Enemy drop pods do give something if you destroy them but I never expected anyone to try and lift an entire pod to the refinery ship. Is that even possible? Does it even fit into the refinery area?