Does Active Thermal Imaging (NDI method) detect all types of structural faults in modern civil aircraft?
No. There is no single NDT method that can identify all types of structural faults in the aircraft. 

Active thermography refers to the use of (thermal) exciters like ultrasound, (halogen and xenon) lamps, eddy current transducers and detecting the defects using that fact that the heat produced is different in those areas, usually using infrared cameras.

Though this is a very effective method for detecting defects, especially in composites, there are some disadvantages as well.


The test specimen has to be 'hooked up' to some form of (thermal) loading device. This limits the size of the tested part. 
This is an excellent method for detecting subsurface defects; however, as the depth of the defect increases, the defect size has to be larger for detection. 
The method requires that the temperature of the region (containing the defect) be uniform. This is a problem especially for materials with high thermal diffusivity like metals, which may require high speed IR cameras.
Though automated algorithms are available for defect detection, most of the (older) methods of thermography depend on the operator for interpretation of results.
The type of excitation technique used can be limited in some cases to prevent damage to the tested part.