Yes, the big problem with Sunless Sea is that fighting and trading don't mesh well with the story elements that are the real draw of the game. It's contradictory because the game is at its best when you're exploring the world that it has to offer, while at the same time punishing you for doing so. You rarely have enough cargo space to be able to afford bringing along a diverse set of items and long journeys are too expensive to risk not turning a profit, so you learn the profitable routes and then come back later to ports that you know require certain items for their events. But this is a slow and dull process that takes a lot of fun out of the game, due to it lacking depth and adding little to the atmosphere; it's a means to an end and you never feel like transporting all these goods has a discernible effect on the world around you (unless you're dealing wih quest-specific goods, which have little to do with how the rest of the trading works).
There's no real choices to make because you either figure out what's profitable, or take risks and die a dull death because you couldn't find a viable port or source of income. It's not hard to do, but it's boring and that's why I recommend cheating a bit, after playing a few games to get a feel for what it's normally like, so that you don't have to deal as much with grinding money. Not too much as you don't want to trivialise the stakes, but enough to avoid having to penny pinch all the time - treat it like an inheritance.

That's also a great fix.

Bingo. I figured out early on how not to get rekt--I've played this kind of deal before--but it came at the expense of turning it into a rote formula and skipping/ignoring most of the story in pursuit of the next port in the known-good route. I might check out that mod. I really did want to like this game for its story and atmosphere, I just found that story time was better spent on other, more exploration friendly games like Endless Sky and the rougelike elements are better served by a host of titles.

I'd recommend at least giving it a go with that mod he mentioned. Despite taking up so much time, the need for supplies doesn't add a lot of tension to the game beyond the first time it kills you. Like you said, once you know how it works it's nothing but tedious. The mod is a big improvement as you still want money to get certain items, ships and tools, but won't have to grind for them because you're not spending tons of money on supplies. Terror and hull damage are also still there and make for more enjoyable problems to deal with.

This should be the mod he's talking about: http://www.nexusmods.com/sunlesssea/mods/4/

Aside from that, there's no point in playing the game as a roguelike. Using manual saves is more fun and has no downsides. And get the zubmarine as early as possible 'cause it's cool.

I never ever ever do any general goods trading in Sea. Coral is hard to miss, I hand in scintillack at Varchas (also hard to miss) and give artifacts to the creep back in London. Two captains' worth of scintillack (say, one meets the Lady or goes NORTH) and I'm rich without ever having visited the Surface (the first captain has to leave a scion so she can't smuggle sunlight effectively anyway).