1. Sure. You could model in some extra complexity there. I'm not convinced it would add to the game, but it's worth exploring!
Oh, I don't want to. The comment on trip length vs. multiple trips was more of an "FYI". I like the way it works now, as it gives trader PCs more flexibility on how they want to run their business - a player won't feel pushed into one option or another over profit margin. The determining factor for small ships is going to be their increment - a 3-5 parsec trip in a class I vessel is going to be hard on the navigator. Fortunately, fuel is cheap so if the need (or profit) to go a long way is strong, a crew can just assume they're going to pay double fuel costs and go with it. That is a relatively minor factor in terms of profitability.
2. Assuming you have at least 4 PCs, you have no crew cost there.
Yeah, in my mind I call that the "Firefly option," because they never seem to get paid.

In theory, a PC crew should still be paying itself. Particularly if the background of the campaign is that they met and decided to throw in together and buy a ship in order to make a living. Besides which, how else are they going to afford all those cool-sounding weapons you put in the book? Heh.
That said, those small ships are designed for shorter runs - they don't even reach 1 parsec in operational range.
Oh, you can put together a Class 1 ship with FTL 4-5, 10-20 CU of cargo space, and an operational range of 5-10 parsecs pretty easily. They're viable small transports...ideal for running very high-end goods (the type that pirates keep an eye out for) or taking on clandestine government missions, say?
But the real reason I focus on them is because a class 1 or class 2 ship has a crew compliment about the same size as a gaming group. That's also the size range of the Millenium Falcon and Serenity, two pretty iconic fictional ships that PCs may be thinking about. But you're probably right, in a "realistic" space trading economy the cargo ships would likely be built as big as is feasible and the crew minimized down to only what's absolutely necessary (i.e., they'd be large Transports in your Starship Construction terms)