I'm wagering on, "most likely". And if not them, Japanese daimyo who as we know learned to make guns from the Portugese right quick. The Sea Lords (and I think that was an 'established term' for some daimyo) were pretty heavily involved in all that. Japanese were big on selling weapons. My gut feeling from reading about the period, mainly from the Sengoku Jidai angle, is that the Sea Lords, being dependant on trade for much of their income would semi-sponsor the Wokou. When not directly engaged. If nothing else turning a bit of a blind eye to their retainers and selling on goods with questionable provenance. I'm betting the modus operandii was to rob Japanese and sell in China and rob Chinese and sell in Japan.
I'm pretty sure one part of solving the problem was for official trading to be established under the Tokugawa and one condition being the Shogun policing his subjects on the matter.
I could probably do better if I dig out the two books I linked too but then I just re-read those all night.
But the answer to your question about the technical aspects seems to have been yes, yes and yes. Ships of many sizes were used, the bigger the more masts they'd have, though usually removed in battle, and yes junks but other types too. Primarily engaging with arrows and boarding actions, but then later on with guns and small cannon, they even used catapults and flamethrowers. Some of the ships were ludicrously large though, several stories high floating palace-fortressesss even (height being an advantage with a mostly small caliber fihgting style). From the illsutrations some of them I do wonder how they weren't blown over. European vessles of the 1500s as I understand where more heavily armed in cannons, more emphasising big guns, and they would not use their ships in line of battle style. Again, as I understand it that was partly the innovation the Koreans under Yi came up with, they focused more on heavy guns, with broadsides and ofc the "turtle ships" even being armoured and pretty much impervious to the opposition. The Japanese was much more into boarding, I don't think it would be too far off the say the Japanese were a bit like the Spanish and the Koreans much like the English (both were underdog seafihgters staving off foreign invaders big on landwrfare). Still IIRC admiral Yi is credited with inventing modern ship combat way before the west really got into duking it out with cannon, I think some British admirals were very impressed with his thinking.