Pennation angle changes with time after exercise and the muscle thickness depends on the ultrasound systems as well as with the person that made the measurements.
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Muscle thickness, pennation angles and fascicle lengths are not a way of studying muscle architecture, they are rather parameters reflecting a muscle's architecture. If the question is whether they techniques we're currently using to obtain these parameters in vivo (mostly sagittal-plane ultrasound scans, very rarely also MRI-based diffusion tensor imaging) are valid and reliable, you might be interested in two very recent reviews (see below). From my perspective, ultrasound has several significant limitations, including a small field of view, tissue compression and user dependency, but it still is a fairly accurate and certainly the most readily available technique.
Aside from limitations regarding 2D ultrasound imaging which has been addressed by Robert, I would look into more variables than pennation angle and muscle thickness. Fascicle length changes of a muscle under passive movement or active contraction may of interest and is readily available to measure though 2D ultrasound.