In effect, they didn't say short barrel shotguns had no militia use (and therefore not protected by 2nd Amendment arguments), what whey said was "we haven't been shown any evidence" and so let the 1934 NFA stand.
The SCOTUS really didn't even quite do that. They remanded the issue back to the lower court.
IMHO a more thorough summary would read like this:
"The militia is within the purview of the federal government. A short-barreled shotgun might or might not be suitable for militia use; we're not sure, since we haven't seen any evidence either way. Since the militia is discussed in the 2A, perhaps the right to possess this gun has something to do with that, or maybe not. At any rate, the militia argument cannot be summarily dismissed. Discuss."
That discussion never occurred, because Jack Miller was killed and Frank Layton plead out.
IMHO the sole thing that's fairly certain about the decision is that it doesn't invalidate the NFA outright. According to what I've read about the case, McReynolds was under political pressure not to do so, and he didn't. The trouble is that, other than the fact that it doesn't throw out the NFA, it's just about impossible to discern
anything conclusive about the decision.
(It's also interesting to note that almost half of the decision consists of quotes from earlier literature about the militia, some of which seemingly has little relation to the topic at hand.)