alot of their shipping were shallow draft wooden "junk" sampans.
Shallow draft junks may have been employed but they weigh less than 1000 tons and wouldn't count for a significant portion of shipping. The Japanese lost over 9 million tons of shipping, over 2,000 merchant vessels, during the war. Most of those losses were in the form of modern tankers (usually 10,000+ tons displacement) and cargo vessels (1,000 - 10,000+ tons displacement).
There's a big registry of the vessels killed here:
https://www.history.navy.mil/research/library/online-reading-room/title-list-alphabetically/j/japanese-naval-merchant-shipping-losses-wwii.htmlYou can reference the displacement for some of these vessels on wikipedia:
https://en.wikipedia.org/wiki/Category:World_War_II_merchant_ships_of_JapanAnd here are some other 1000+ ton modern support ships the IJN used:
IJN ammunition ships:
http://www.combinedfleet.com/Kyuheikan_c.htmMaru class hospital ships:
http://www.combinedfleet.com/Hikawa_c.htmOther supply ships:
http://www.combinedfleet.com/Kyuryokan_c.htmI don't know about the idea that they "despised" logistics, I'm not really sure what that means, but the Imperial Army and Navy did resist cooperating with one another on logistics and vessels on either side would sometimes be underloaded during a trip because they wouldn't collaborate and load supplies from the opposite branch. But they definitely didn't rely mostly on small, wooden ships for strategic logistics.
Subs are super-fragile, and thus really shouldn't get into a firefight. Giving them guns just encourages them to do that. (See also AA guns.)
It also hampers the crash depth time (have to make sure the gun barrel is tied down) and underwater speed due to drag. So yeah, I don't think it's worth it.
AA guns are nice for when you know diving will get you killed (i.e. there is a destroyer and it's seen you and you're outrunning it because if you dive it will kill you or you can't dive because of damage), usually diving is the right choice but you just have to trust captains to make the correct choice given the situation. That's actually something that's worth noting, our subs will outrun their smallest vessel on the surface, they really need a fast destroyer to even get our subs to dive unless they get caught off-guard.
This is true but we can afford to take an offensive advantage at this early stage when the enemy has no good counter. I don't know how many torpedoes the sub can carry but the subs will be used to kill merchant shipping and the Cannalans don't have armed merchant vessels that could threaten our subs on the surface and I doubt their big expensive cruisers can be used to escort convoys of merchants very often, which is the perfect environment for a deck gun. Saving torpedoes means tremendously increasing the endurance of the sub at sea, that could be a tremendous force multiplier while the enemy is caught flat-footed. If we're still going for a missile revision next turn we can just remove the deck gun for free to give us that defensive edge back.