In spite of poor measurement precision, the test results are quite convincing:
the table on the wiki
http://dwarffortresswiki.org/index.php/DF2014:Minecart#Numbers_behind_the_sceneappears to be incomplete:
I ran a cart through a seven-tile water trough, at different depths. At depths 1-6, speed didn't change much: 42 tiles in 28 steps at 1-2/7 vs. 41 tiles in 28 steps at 5-6/7; since the cart spent five steps under water, this more or less agrees with the reported friction of 100 per water depth above 1.
However, while moving through 7/7 water, speed went down radically: the cart spent seven steps in the trough, two on the ascending ramp (costing it another ~5000 speed) and took 60 steps to move 43 tiles, i.e. ~72.000 arbitrary speed units. If water imposes per-turn friction, that implies 7/7 water has a friction not of 600, but of ~10.000 (subtiles/stepē), as much as a high-friction track stop.
I tried it both with closed ceiling and open space directly above the water and the results are the same, the higher friction is an effect of the "full" water square.
As another outcome, i'm now reasonably sure that minecarts take on water (and probably magma) when moving at <10.000 speed while submerged in sufficiently deep liquid (7, maybe also 6). Naturally, hitting such a low speed is easier when moving through a "full" tile, thanks to the enhanced friction. Tests: highest-speed roller cart spends two steps in 7/7 water, emerges at 30.000 speed, takes on no water. High-speed roller cart spends eight steps in originally 7/7 water, takes on water after three steps (just under 40.000 - 3x10.000 puts it below 10k), emerges at about 8.000 speed. Loading of water and emergent speed were the same for a wooden and a nickel cart, so the slow-down is not an effect of the weight gain but only of "high-water" friction.
Unless someone can come up with better numbers/explanations, i'll edit these numbers (10k friction from highest water, 10k maximum speed for loading water; absent better data, i'll note that maximum magma empirically has even higher friction than highest water) into the wiki in the next days.