I'm curious what sorts of procedures people have going on in their campaigns.

Do starships have transponders? If so, are rogue traders immune to the laws concerning tampering with them?

How long do docking procedures take for ships 1 mile long? How long does loading and unloading take? How much is this increased when Halo barges are your chief vehicle?

Do ships maintain their void shields while at dock? If not, at what point do they raise them when leaving?

What kinds of docking mechanisms are in place? All the different ship classes have different types of cargo bay doors.

Sure, this is what I use:

1) Ships don't have automatic transponders. You are, however, expected to identify yourself upon reaching reasonable vox range of a colonized planet, space station, or if queried by an authorized Imperial Agency (Navy, Arbites, Inquisition, Administorum, Planetary Security). Its also worth noting that every vessel fairly unique energy signature that can be pick up from focused Augury range, and warp-capable vessels have a fairly unique energy bleed from the warpdrive. Both of these are often catalogued by local authorities.

Falsely identifying your vessel (such as by giving the wrong Adminstum registration code) is a severely punishable act. When in Imperial space, this law applies to Rogue Traders as well.

2) It can depend greatly on the efficiency of the station, but the general approximation I use for well run Imperial stations is a smaller vessel (freighter or escort) can dock about an hour from the time it gets within 1 VU of the station. A cruiser or bulk freighter is going to take two hours, or double that if the station isn't equipped with tugboats.

3) Unloading varies wildly depending on the efficiency of the station and the efficiency of the docked vessel. An un-heavily modified normal sized freighter docked at a good commercial station carrying its cargo in Administorum Approved standard cargo containers could unload in, say, a day or two. A cruiser with a maze and a compartmentalized cargo hold docked at a navy station might take a week or more to unload its cargo. A vessel in orbit unloading by lighter could be there for weeks. (one would typically load and unload at the same time then, so the tenders don't spend any time flying empty.

4) Although there's nothing physically preventing one from raising Void Shields while docked, it would be seen as rather odd and wasteful of fuel. You'll definitely get a citation if your drawing power from the station to do so. A normal vessel would activate it's navigational shields about the time they pass the 1 VU mark from the station, and raise Void Shields only when they're expecting an attack.

5) It's 40k, so I assume super-massive chains are involved to secure the ship to the station, perhaps with electro-magnets. Pressure-docks like those used on airliners (but way, way bigger) would seem to me to be the most common. By being well oversized to the doors, they can be adapted to most vessels.

Do starships have transponders?

But if you do not emit an identifying signal in an inhabited system, you will likely be assumed to be hostile, probably an raider (if solo) if an invasion force (many ships).

Thus systems will likely mobilize whatever space defence forces they have when you enter the system with identifying yourself.

If so, are rogue traders immune to the laws concerning tampering with them?

How long do docking procedures take for ships 1 mile long?

How long does loading and unloading take?

Do ships maintain their void shields while at dock? If not, at what point do they raise them when leaving?

What kinds of docking mechanisms are in place? All the different ship classes have different types of cargo bay doors.

Mostly they go into a stable orbit, and move goods and people via small crafts.

I'd think that moving goods via small craft is inefficient. Orbital docks seem better, though I'm sure we've all done deals in primitive systems, which brings up the logistics of bringing to orbit millions of cubic feet of trade goods.

We have many cases in fluff (Black Library, codex and FFG) of commercial void stations - so there has to be some level of docking and unloading. Granted, the orbital station is still dropping the goods planetside by small craft - but they have room for lots of very large small craft and, more importantly, can free up the transport to begin it's next multi-month voyage while it runs 24-7 to get the Imports planetside, and new Exports up to await the next ship.

Yeah, that's the way I picture orbital docks, mostly warehouse space and docking bays, both for shuttles and the transports.