
There isn't much of a reason you would catch flak for having Maelstrom flags while riding through Thanalan.
The three city-states(four if you count Ishgard) aren't at war with each other, and have shown no real desire to contest city-state borders at all.
Nanamo even went to council with the other two city states, asking them to assist Ul'dah in its transformation when she had wanted to step down and let the city be ruled by the people. That's not something you do if you were at war or cold war with a bordering nation.
The three city-states(four if you count Ishgard) aren't at war with each other, and have shown no real desire to contest city-state borders at all.
Nanamo even went to council with the other two city states, asking them to assist Ul'dah in its transformation when she had wanted to step down and let the city be ruled by the people. That's not something you do if you were at war or cold war with a bordering nation.