I just checked again.
I have a shared list with the id 771682. In my settings I saved the following custom CSS (one general rule, and one rule specific to the list):
The result looks like this:
The shared list has the public URL https://checkvist.com/p/UV9IHRjo2QWFWQqS5rszuS. If I open that URL while being logged in to Checkvist, the custom CSS is applied and the list looks just the same as above. However, if I open that URL in a private/guest browser window or after having logged out, the list looks like this:
So, yes, the custom CSS is applied to shared lists, but only for me, not for someone I share the list with - at least if (s)he has no Checkvist account or isn’t logged in (I don’t know, and cannot find out, what the list looks like for someone who has a Checkvist account and is logged in, but did not set the same custom CSS).
I hope this clarifies the issue.