You asked if you should take clogging into account.
Take clogging into account by designing the facility to trap sediment and flotables upstream of the outlet structure rather than in the pipe/orifice/weir/restrictor that forms the hydraulic control for the facility. In many cases you can use a submerged pipe or orifice upstream of the restrictor that will trap flotables at the water surface, and provide a sump for sediment. In a few cases I've seen a floating boom used to trap flotables; this makes sense if the restrictor is an open-channel device like a weir or flume.
With these clog-prevention design elements included, I would not include clogging when performing hydraulic calculations to size the flow restrictor, so long as an overflow is provided as noted by Terryscan.