When you are being questioned by authorities, even if you are 100% clear/not guilty in the matter the simple fact of the matter is that it is very unlikely that you will be 100% accurate in your testimony to the authorities. Little details (even when correct) can be twisted by the authorities who have an incentive to get a conviction. So the fifth amendment was created to give legal protection to individuals who do not wish to testify or talk with authorities themselves and allow them to utilize an impartial 3rd party lawyer to manage the conversation flow.

A jury in a criminal case is not supposed to hold any weight to someone taking a fifth amendment plea to not talk (since it's a provision really meant to protect the innocent) but with human nature that's unfortunately not the case.

However, since this is a civil case I don't know if the legal system has to be neutral in a Fifth amendment plea. If not that would help Waymo's case, especially since Waymo does have evidence that he downloaded these documents. So Him taking the fifth is just to make sure he doesn't do anything himself that will spawn a criminal conviction later.

(IANAL)