@Andrzej-Jaworski Possibly yes if want to try the LuaScript plugin.
Install the LuaScript plugin from the menu Plugins -> Plugins Admin which is just 2 DLL files approximately 1 MB in size. Once Notepad++ is restarted then from the menu Plugins -> LuaScript -> Edit Startup Script which will open startup.lua in the editor.
Add this code:
local function EventReady()
-- Set SC_CURSORARROW instead of SC_CURSORREVERSEARROW.
for i = 0, editor.Margins - 1 do
editor.MarginCursorN[i] = SC_CURSORARROW
end
end
npp.AddEventHandler('OnReady', EventReady)
Notepad++ needs restart before the code in startup.lua will be run.
I tested it initially without the ready callback event though consider as a good idea to use it so that Notepad++ is in a ready state before applying the user code.
It appears to work OK as I typically set an inverted arrow which is translucent and I do not see the white reversed arrow over the margins. I have not experienced the black box so cannot state that it is a solution to your problem. If the margin count changes due to plugins adding margins then not sure what may happen though might be better than a black square entirely for all of the margins.
If you have PythonScript plugin or similar, then possibly could use similar code for that language.