Underground downspout drainage: Water standing in my brand new drainage pipes
A backslope in a drainage line from day one is bad workmanship. Over the years it might settle a little more and become worse.
THe question is not that of harboring bugs. It's a matter of degraded capacity of the pipe.
When cleaning anything including baby diapers, it is better to sweep off or scrape off as much solid and semisolid material as you can first. (1) Less cleaning fluid or detergent needs to be used, (2) Less of a mushy mess which in turn means that bleaches or disinfectants will be more effective.