Is Fluid Structure Interaction considered in aircraft design?
Just one example: Good designers put the aileron pushrods away from the elastic axis of the wing to enable the deformation of the wing to create a damping deflection of the ailerons. This is especially helpful for high aspect ratio wings:



When the wing flexes, the pushrod will not be compressed, so will become relatively longer than the surrounding wing structure. This will create a negative aileron deflection which works against the lift force which flexes the wing in the first place. Doing this is particularly helpful in damping wing flutter.

Generally, the engineers make sure that every aircraft component works as intended even when the structure is deformed. Another example: To compensate for differences in the thermal expansion of different components, pushrods in glass fiber fuselages have two halves, connected by a pivoting lever, so that changes in their length will compensate.