I changed some code so you guys could fool around with this (you guys = anyone with a debug build)
Go into a debug build and bring up the debug console (shift + backspace or something like that). Then type in "neb2". You will see a list that looks something like this:
neb2_fog : set near and far fog planes for ship type X
where X is an integer from 1 - 11
1 = cargo containers, 2 = fighters/bombers, 3 = cruisers
4 = freighters, 5 = capital ships, 6 = transports, 7 = support ships
8 = navbuoys, 9 = sentryguns, 10 = escape pods, 11 = background nebula polygons\n
neb2_max_alpha : max alpha value (0.0 to 1.0) for cloud poofs. 0.0 is completely transparent
neb2_break_alpha : alpha value (0.0 to 1.0) at which faded polygons are not drawn. higher values generally equals higher framerate, with more visual cloud popping
neb2_break_off : how many pixels offscreen (left, right, top, bottom) when a cloud poof becomes fully transparent. Lower values cause quicker fading
neb2_smooth : magic fog smoothing modes (0 - 3)
neb2_select : where the first # is the bitmap to be adjusting (0 through 5), and the second int is a 0 or 1, to turn off and on
neb2_rot : set max rotation speed for poofs
neb2_prad : set cloud poof radius
neb2_cdim : poof cube dimension
neb2_cinner : poof cube inner dimension
neb2_couter : poof cube outer dimension
neb2_jitter : poof jitter
neb2_mode : switch between no nebula, polygon background, amd pof background (0, 1 and 2 respectively)\n
neb2_ff : flash fade/sec
neb2_background : rgb background color
Fool around with the top one (neb2_fog) and see if you can find a value that works...
I can probably set up a table or something you can put the values into for a couple weeks.
Also, note that neb2_fog seems to be incorrect. Here is a table of the current values from the source. The first value is the "near", second value is the "far", the index starts at 0 (so super capital ships would be 11, rather than nebula polygons.)
{0.0f, 0.0f}, // SHIP_TYPE_NONE
{10.0f, 500.0f}, // SHIP_TYPE_CARGO
{10.0f, 500.0f}, // SHIP_TYPE_FIGHTER_BOMBER
{10.0f, 600.0f}, // SHIP_TYPE_CRUISER
{10.0f, 600.0f}, // SHIP_TYPE_FREIGHTER
{10.0f, 750.0f}, // SHIP_TYPE_CAPITAL
{10.0f, 500.0f}, // SHIP_TYPE_TRANSPORT
{10.0f, 500.0f}, // SHIP_TYPE_REPAIR_REARM
{10.0f, 500.0f}, // SHIP_TYPE_NAVBUOY
{10.0f, 500.0f}, // SHIP_TYPE_SENTRYGUN
{10.0f, 600.0f}, // SHIP_TYPE_ESCAPEPOD
{10.0f, 1000.0f}, // SHIP_TYPE_SUPERCAP
{10.0f, 500.0f}, // SHIP_TYPE_STEALTH
{10.0f, 500.0f}, // SHIP_TYPE_FIGHTER
{10.0f, 500.0f}, // SHIP_TYPE_BOMBER
{10.0f, 750.0f}, // SHIP_TYPE_DRYDOCK
{10.0f, 600.0f}, // SHIP_TYPE_AWACS
{10.0f, 600.0f}, // SHIP_TYPE_GAS_MINER
{10.0f, 600.0f}, // SHIP_TYPE_CORVETTE
{10.0f, 1000.0f}, // SHIP_TYPE_KNOSSOS_DEVICE
If you can confirm that the table is right, rather than the description, I'll update the description so it's correct.
Edit: Note that I made the necessary change awhile back, so you should be able to play around with all the fog stuff in any recent build.
Edit 2: And if this didn't clue you in, fog distance seems to be set depending on the ship type, rather than with just some global value.

Kind of unfortunate as I think it would look more realistic with the latter.