Given that historically the Chinese relied on local militias well in to the 1800s, I'm not so sure that there was a particularly clear divide between civilian and military weapons, particularly in Taiwan, especially in the 1600-1700 time frame.
One possible approach would be to do an analysis of the weapons taught in the various southern traditional martial arts. I realize there are some problems with that approach, but maybe the percentages of say, staff and hoe forms in Choy Lay Fut versus the number of broadsword forms might give you some insight.
I'd also be inclined to think that Taiwan might be a bit of an outlier from the rest of South China, and while it might be a more "backward" area it might therefore been better armed. I don't know if you've read "Rebels and Revolutionaries in Northern China". I think that is the title. I bought it years ago while I was living in Taiwan and subsequently loaned it to a guy and never got it back. Anyway it was a study of the dynamics of banditry, rebellion and revolution in 3 northern Chinese provinces in the 19th and 20th Centuries. These provinces, I forget the exact three, had a long tradition of unrest and banditry. I remember a couple of points in the book that might be relevant. One, although he did not elaborate on this point, the author did note that the "rebellious" reputation of these provinces was similar to Taiwan's and the second was although they were extremely poor provinces the inhabitants were very well armed. In fact, the peasants were criticized by government officials for their propensity to buy guns and swords rather than invest in agricultural improvements. Of course, the author explained what this was not completely irrational behavior on the peasants' part, but the main idea here is just because the civilians may not have been wealthy, it doesn't mean didn't buy good weapons if they could.
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