If this is a proposed design, my first recommendation would be a
redesign to reroute one or both of the structures to avoid obstruction
and maintenance issues. Perhaps the box could be transitioned through a
squash box, or the pipe could be rerouted above or below the box.
Failing that, there should be access from the ground surface upstream of
the cross pipe to remove debris when the system fails.

If this is an existing storm drain or combined sanitary/storm drain that
receives surface stormwater flows with debris, then there are safety
issues in addition to modeling issues. I am familiar with two similar
examples, both of which trapped debris that obstructed flow.

Modeling assuming a sealed pipe upstream and bridge pier with debris
loading might be an approach, but in this case there is more pier than
conveyance section.

Neil Jordan
NJordan@EXPONENT.COM