I was reading through the ship component aquisition rules in the rulebook, and was confused in the example they use to explain it. In the example on page 274, it talks about a RT trying to improve his macrocannons from common craftsmanship to good, but this doesn't seem to make any sense because I have yet to see any information in the rulebook that explains how craftsmanship quality affects ships components at all. DO they work like armor or weapon quality? That seems to make little sense because of the nature of ships, but any clarification would be greatly appreciated.

The short answer is they don't have any effect, yet. Hopefully official stuff will be in Battlefleet Kronus.

If I remember correctly "Into the Expanse" has effects for the quality of some of the components listed in there. However, it doesn't give any general rules (though presumably it would have the normal modifier on acquisition rolls).

This was a question asked when RT first came out. The answer was something along the lines of:

Quality does not have a set/definitive bonus. Quality components are more extravagant and luxurious, while poorer ones are worse looking, and a GM may assign appropriate bonuses as desired. As an example:

Armored Prow - Poor quality means the extra armor is rusted and bolted on haphazardly. A good quality armored prow is neat and trim, with fancy glyphs and sigils engraved on it. A best quality armored prow is perfectly done with additional bastions and buttresses and psalms to the Emperor.

The better quality armored prows might give a slight bonus to social interactions with other ships of the Empire, while the poor quality might give a slight negative.

As has been said, quality in this case doesn't necessarily confer any hard bonuses, however it can be a good idea to give "soft" bonuses.

Social interactions are a big one. Poor quality causes peers to look down on the trader and their ship, good and best quality causes them to treat them with more respect.

A lot of fluff descriptions can and should be altered depending on the quality. When trying to rapidly accelerate you may describe for a poor quality engine "the ancient engine sputters and starts as it attempts to gather up speed".

If the ship had many poor quality components I would emphasize the amount of breakdowns, perhaps even forcing them to deal with some of them.