They interpret 2A as a collective right for the purposes of explaining why they (and note that this specifically refers to the national ACLU organization!) do not step in to defend it.
However, they never argue in court against 2A. Nor do they prohibit their member state organizations from taking a different position - and many do.
Yes, ACLU is a broad "civil liberties" organization. But there's no definitive list of civil liberties, and different people have different opinions on this. The fact that SCOTUS ruled on it doesn't change matters - SCOTUS rules on whether something is a constitutional right or not, not on whether something is a civil right or not. The latter is inherently a subjective assessment.
I hear what you're saying, but it's clearly at odds with the position described at https://www.aclu.org/blog/speakeasy/heller-decision-and-seco... .
They explicitly interpret 2A as a "collective right," whatever that is. They also state their disagreement with Heller and presumably any number of lower court decisions in line with it.
Organizations like the EFF never claimed to be broad-based "civil liberties unions," so that's why I feel it's appropriate to hold them to different standards.