Shuttles can be purchased and stored in shuttle bays as shown before, but now you can also board the shuttle and see the inside of it and the crew inside the shuttle like this:
Shuttles can dock to shuttle bays, airlocks, and other parts. A shuttle can be used to board enemy ships to make a surprise attack or to send help to a distressed ship, also to evacuate ships in danger, there are multiple uses for shuttles, but also you can dock using your main ship. By doing so, you may put the whole ship at risk if something goes wrong, so using a shuttle is an option given to the player, to buy or not to buy.
A space ship have many modules but you will have to choose what kind of modules you may want to have , capacity is limited so better weapons?, more storage? more energy generators, more shields? so many options, and shuttles is one more of them.