What's the fastest way to gain Echoes in Sunless Sea with Zubmariner?

Early captains should focus on getting legacies.

Last request quest chain in Venderbight and Pulse of the Principles quest chain in Port Cecil are both extremely profitable once completed, and will force you to explore a bit. You can complete both chains in a reasonable equipped Phorcyd corvette pretty easily, and there's enough low hanging fruit to fund that corvette too.

Later captains will be able to afford a cargo ship much earlier, these will benefit from the salt lions stone pickup more as well as shipping coffee to Vienna and the classic London (wine) - Empire of Hands (wine - darkdrop coffee) - Irem (darkdrop coffee - parabola linen) - London (sell and repeat) trade route.

Bit early to say for Zubmariner although there's definitely an easy 1000 echoes to be had trading meat from the Gant Pole to the Chelonate. You can also earn really good money farming dawn flukes if your vessel is up to it.

There's one opportunity that Zubmariner added that's very exploitable, with a catch.

Ambiguous Eoliths can now be bought at Anthe for 30 each. When sold to the Alarming Scholar, they give either 1 or 70 echoes, on a 50/50 chance - so an average of 35.5, for a profit of 5.5. This seems tiny, but Eoliths are Curiosities and take up no hold space. You can buy 10000 of them in a single run (I have done this; the numbers on the icon get scrunched, but it works). At a profit ratio of 15.5%, you can multiply your money very quickly - although because it's multiplication, you need a fair amount of starting money to make it worthwhile. If you have less than 50k echos, I'd do the Cumeaen Canal loop at ~8000 echos each to gain echos faster first.

The huge catch here is that no one wants to click through menus 10000 times to sell each one individually. Using a mouse-clicker program is thus a requirement for this scheme, which may kill it for some. Also, even when automated it takes a long time to sell; going through 10000 takes roughly a couple of hours. Earning a million echoes will probably require running it overnight. Another strategy is to keep a hoard of 3000 or so that you can burn in London when you have some down-time and want to do something else; nothing requires you to do it all at once, after all.

Personally, I use AutoHotkey. Here's the section from my macro file that pertains to Eolith trading. Note that this is for 1680x1050, it's likely you'll have to tweak the exact click positions:

SpamClick(count := 10) {
  Loop %count% {
    Click
  }
}

ToggleAction(fn) {
  static toggle = 0
  if (not toggle) {
    SetTimer %fn%, 100
    toggle = 1
  } else {
    SetTimer %fn%, Delete
    toggle = 0
  }
}

TradeEolith(count := 25) {  ; The count param controls the ratio of regular actions to re-syncs
  ; "The Alarming Scholar", re-sync if we fell out of the menu
  ; Doesn't click on anything else otherwise
  Click 1160, 840    
  Loop %count% {
    ; "Go", Low side of the button, prevents issues if we're in other menus
    ; This assumes there is exactly 1 of a Zee-Story or Memories of a Distant Shore
    ; to trade to the Scholar, because they appear above the Eolith. If you have both,
    ; sell one set off first.
    Click 1315, 930
    Sleep 60           ; Extra time for the next screen to pop
    Click 1315, 990    ; "Continue..."
    Sleep 40           ; These sleep numbers are *very* fiddly, I often have to adjust them up
  }
}

NumpadAdd:: Reload  ; Useful when making changes

NumpadEnter:: ExitApp  ; It's important to have an emergency exit button, if things go wrong

*NumpadDel:: ToggleAction(Func("SpamClick"))

NumpadIns:: ToggleAction(Func("TradeEolith"))