Are your concerns more than just theoretical? I've been developing in Node for a long, long time now and have never had any issue with any of this. Take source control for instance: isn't the first thing you do to put `node_modules` in your gitignore?
What makes you think they're just theoretical? Are you insinuating that I'm just here to argue arbitrary crap for the hell of it?
Also, gitignore does not work in SVN (*omg he uses SVN! the shame!), and the node_modules do actually have to be included in the source since the runtime is disconnected from the internet (intranet app).
Since for some reason that's what everyone else is doing in this thread ("I once read the Node documentation two years ago and am therefore in a position to make grand and sweeping judgments about it") I'm afraid I lumped you in with that crowd. Apologies.