They might very well be. As i understand the process, and I am no expert, these issues are discussed before hand, a clerk is assigned the task of writing the opinion and consultation with his/her Justice is a fairly regular occurrence. This of course varies from Justice to Justice.
I've been a judicial clerk, a job I absolutely loved. The role of a Clerk depends extensively on the Judge. Some Judges use their clerks as well-educated secretaries, some essentially let them be the judge. Other judges, such as (allegedly) Richard Posner, don't let their clerks touch their judicial opinions, and instead use them as federally-funded researchers for their outside writing of books and law review articles.