1) So, I read somewhere that Docking Bays are to allow ships to dock inside other ships, whereas Docking Ports are to allow ships to dock at spaceports. Correct thus far?
2) Is there a way to determine from the ships' specs which ships have Docking Bays? I can't seem to tell. Or is this by class?
3) How can I tell if one ship is small enough to land in the other ship? I can't find a weight for the landing ship...only what it can carry. So, the receiving/container ship specs I can find, but not the ship that's to land.
4) Say SmallShip which is full of stuff is inside LargseShip which is empty (other than SmallShip being in it). Would LargeShip be weighed down by the weight of SmallShip PLUS its cargo, or just SmallShip's weight itself.
5) Is there ANY way to dock a ship with another such that they are connected outside...i.e. such that there would be an airlock to go from one to the other ship? If so, is it possible to move such connected ships together? Also, would you be able to load up the two ships such that both of them had stuff in them? Or would the connection somehow affect how much they could carry?
1) Docking ports allow you to travel from a capital ship to the entrance room of a different capital ship or space station (theoretically) but yes, you are otherwise correct.
2) If you see this icon below the ship image on the rules page, it has a docking bay:
3) To understand if a ship can fit inside another, you compare the weight/volume of the ship you want to dock with the weight cap/volume cap of the ship with the docking bay. If either of the numbers are larger than the weight/volume cap, it cannot be docked.
4) Large ship is only concerned about the mass/volume of the ship being placed inside, the weight of the items and other material inside the smaller ship are ignored.
5) Under normal circumstances, you cannot move two ships at once. There is no connecting tube/docking port/coupling system implemented. If two ships are in the same square you may freely move between them, but once you move one ship you lose access to the other. The only exception lies in squadrons. You can group fighters together, or certain transports in the freighter class. Full details are listed here: NPC Squad Rules
I hope I answered everything you asked. If not, feel free to clarify on what more you need.
Hangar bays allow ships to store vehicles. THey work identically to a docking bay except for vehicles.
Repulsors denote that the ship can travel into atmosphere. Some ships are limited or too ungainly to reasonably allow this.
Landing capacity is similar, and defines that the ship can actually land. Yet again, there are ships that cannot, and most of these fall into the capital ship classes. The majority of the ships that do not have this make up for it with a docking bay.
I spoke to Jevon Lambright via DM some more about Docking Bays vs. Hangar Bays. I am copy/pasting what he said here to help others out there.
"If you have a ship with 1 docking bay, you can fit as many ships into it as the larger ship has space. Hanger bays do not affect the space for. If the ship does not have a docking bay, it cannot transport ships. No way to do it whatsoever."
"Hangar bays only allow you to transport vehicles."