First congratulations to Fredrick. 
i do like the idea of giving the player control over the baggage system as you have done. I’m not keen on the lines showing the links - in the last image it looks lit it could get congested and confusing. Could you instead just have the linked object highlighted. For example, clicking on the baggage bay highlights the baggage bay in green, but also highlights the stands and checkin desks that are connected to it (maybe in red, or blue, or another obvious colour that works)? I think this might be nicer visually, and easier to see which objects are linked.
Given the checkin desk is linked to a baggage bay and the baggage bay is linked to a stand, then the checkin desk must also be linked to stands too (via the baggage bay) - that is passengers then must go to one of the linked stands for their flight. Is there value and ability to show the stand a checkin desk is linked to when clicked on, same with a stand - not only show the baggage bay but also the checkin desks?
Can gate desks be assigned to stands in a similar way, so we can assign more than one gate desk to a stand- for larger flights this would speed boarding. It’s pretty common in airports to have this. Also for small stands with small planes, sometimes only have one gate desk for two or three gates.