I don't think the site owners are going to get into trouble, at least not in the long run (although there may be some initial knee-jerk attempts to shut them down).
Distributing programming instructions to make gun parts on a 3-D printer isn't fundamentally different from distributing plans, instructions or engineering drawings on paper, and as far as I know, that's legal.
It's up to the end user to make sure he doesn't run afoul of the law by producing something he shouldn't.
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