My opinion is that grouping all tandems by wheel size is a mistake. There are good and bad bikes using all sizes. Same with frame material.
The first decision to make on a custom bike is what tire type fits your riding. That could impact the wheel size selection and will dictate the type of frame and components you chose. Bad tire selection can make any bike faster/slower, comfortable/uncomfortable, reliable/unreliable depending on how they are used.
All but the worst bikes will not slow you down. Bikes are not fast - riders are. We have owned different types of tandems and are most happy with our final choices. While we enjoy them much more than our previous bikes they are only very marginally faster.
Over the past 10 years and four tandems of tandem riding I feel are bikes have improved a lot but we have aged and gotten slower - go figure.