I do believe the Wako (because despite the name and claims, the majority of these were actually Chinese) problem was primarily a result of the shortsightedness of denying their populace access to sea trade. IIRC even fishing in anything but the smallest craft wasn't even allowed. This lead to piracy since the coastal populations kinda depend on the sea, which in turn meant the powers at be focused even more on using the canals as interior channels since they lacked the will or ability to do something about coastal trade. In essence I think the canals are in part both cause and effect of the piracy.
Oooo... don't let a Korean catch you saying that. It was the Koreans themselves who developed the naval forces to beat the Japanese, fact is, much of it was on the shoulders of one man whose patience in the face of corrupt stupid shortsighted politics verges on saintly, Admiral Yi. I can't recall exactly how much Ming China contributed, but the major contribution to sea-warfare was Korean, e.g. the Turtle ships and putting more emphasis on cannon over boarding.
Very nice byte sized overview of the Korean side of that conflict through the POV of the man who arguably won the war.
http://bit.ly/1FkP5ZO