A surprising number of jap merchants were pretty heavily armed.
http://ww6.enjoy.ne.jp/~iwashige/modellist.htm
This came up on another forum, and I started out opening the thread with the premise that I thought ships were overarmed. I shortly decided that I was wrong. Roughly speaking, jap merchants were divided into thirds. 1/3 commandeered by the IJN, 1/3 by the IJA, and 1/3 remained under civilian ownership (but still government control).
All the IJN ships were armed at some level. Many heavily. Larger composites frequently have 6-8 DP guns (3 to 5 inch DP deck guns), and as many 13mm MGs (later many converted to 25mm guns). Ditto the IJA.
Their accuracy is another matter

The trouble with small-arms (MGs) is that they don't bump off the deck crew as they should.
Here is what an SH4 ship—Nagara Maru—looked like in RL:

4 DP deck guns, 4 MGs.