Can all dynamic analysis (ex. Response Spectrum, time history, Harmonic, etc..) be performed on underwater piping correctly while using AutoPIPE?
Yes, AutoPIPE has a nice interpolated spectral report found in the "Analysis Summary" sub-report. This reports the intersection of the modal frequencies with applied response spectrums but also calculates the ZPA acceleration.
Again, AutoPIPE calculates the Zero Period Acceleration, (ZPA) which can be defined as Static Seismic (Sg) Load at ground level. This is same as Peak Ground Acceleration (PGA)
Dynamic "Response Spectrum" Analysis