It is generally always better to be conservative in your analysis and design, especially when it comes to flood events. Accordingly, the loss of conveyance due to bridge railings should be considered when defining the high chord geometry at a roadway crossing when using HEC-RAS.
As shown in the photo below, you can see that the bridge railing has a sizable effect in creating additional backwater upstream as the water surface elevation rises at the bridge structure.
The upper portion of the guard rails should be included, even if there are openings within the guard rails.
It should be assumed that guard rail openings will fill up with logs, debris, and other trash during a flood and reduce and/or prevent conveyance.