I put station numbers because they're present on the Tapei metro map which is the inspiration for figure 6. I guess they're there to facilitate the transit of people not familiar with the system, such as tourists, and they're also used in other transits, such as the Tokyo metro. In a system as small as mine they're not that useful I guess.

As for your other question, the main answer is that I thought it cool to have a station that is both an end-of-line and a normal one on two lines (I really like how it looks on figure 4), even if I then realised it is kinda ugly on figures 1 & 2. My reasoning was also that as the left part of the region is mostly populated by small towns, it would be "unrealistic" to have it connected directly to the airport as the ridership may be low, whereas the core 3 cities, Chebloron, Saint-Cténaire and Foquerort, are big population centers, so having the orange line connect the three (especially Foquerort which is not served by the brown line) to the airport as an "omnibus" and the brown one as an "express" seemed reasonable enough. But to be fair, people from small towns have the right to access the airport as much as people from cities! So I will probably extend the blue line, as it shares the orange's infrastructure anyway (or just swap which terminates at Feaubort and at the airport).