Finally my time to shine haha ! Professional paleontologist here, the answer is "yes, but"

We do undersample EVERYTHING solely due to how rare and exceptional the fossilization process is. We especially undersample anything other than hard mineralized tissues, so yes, a lot of metamorphosis is forever lost, but that's a drop of water compared to the universe of soft bodied creatures that we will never get to know...

However, we are not that clueless, for several reasons. First, using a kind of uniformitarian thinking, we can speculate that ecological communities were similarly structured to those we know today, and as such estimate what we're missing, particularly how much we're missing. But also, and perhaps the most exciting, we do discover new things everyday, and I don't think that people grasp how much our discipline has evolved and been changed by new technologies in the last 20 or so years. Scans and 3D imaging techniques allow us to examine the most minute details of fossils previously hard or impossible to study, and methods such as Synchrotron powered X ray fluorescence allow us to unravel unprecedented levels of details and information on soft tissues. I had the opportunity during a research conference to discuss the results of a young researcher working on amphibian metamorphosis on specimens about 300 million years old, using these technologies. He was able to study very early stages of development, and observe structures such as intestines, eyes, and even the various layers of skin !

In conclusion, yes we definitely undersample metamorphosis, but we probably don't underestimate it that much today, because we can estimate how much we're missing. Furthermore, new technologies allow us to study unprecedented levels of detail, including unseen before soft tissues.