A stupid/naive question. Why does this affect SpaceX? They have their money(The IPO) Any third party trading value does not change that. Sure there may be individuals, officers of SpaceX who hold these instruments who will be negatively affective, but the company itself? My best guess, it makes it harder to get loans in the future.
It's better described as "it increases operational risks to SpaceX". When they face some future difficulty, the odds they can come out of it are lowered. Which is itself a factor that partners consider, including employees, because obviously people prefer to bet their livelihoods on more of a sure thing.