The IRS may not consider an LLC a corporation for tax purposes, but this has nothing to do with whether a court will consider the LLC as an entity that provides its owners with liability protection. Courts do not give IRS classification any weight. Tax liability and liability for other corporate debts are not the same thing. (It is a common misperception, though.)

However, that is not the issue here. The ACLU is arguing (rightly) that even though these entities are corporations, they are acting as agents of the government, and thus should be required to follow laws pertaining to government agencies.