With commercial ships today, any size is fine: shape isn't related to that much. (Alas, with today's ships, you can easily count window rows - it's in silhouette where it becomes irrelevant whether a ship is 75 meters long or 300.)
Many Trek ships are fine in this respect, too: while the Batris family of ships does have windows, it doesn't exactly have window rows, and thus the same shape could represent ships of wildly varying sizes. Nothing much establishes a scale there, after all: there's no "standard container" involved, no docking port, no bridge dome. Just windows of unknown and arbitrary size.
The Merchantman is pretty easy, too. It has a dome, which may be taken for a bridge, and allows for the ship to be kilometers long if we want (it just happens to be a really large bridge, then, but since we never see the interior...). But the dome may be a sensor atop a bridge, too, and this bridge might snugly seat but two guys. Pretty much as we see happen in ST3:TSfS.
Fifty meters is certainly an option, then - and since we see cargo stowed in the very control room, not an unlikely one, either (else wouldn't it all be in the putative holds elsewhere?). But there's little problem with a length of 25 meters, either: this would essentially be the Cardassian runabout, only with broad wings and big "rockets" but with pretty much the same size of control cabin.
Timo Saloniemi
