In the MIKEZERO Toolbox, you can compute time-averaged maps from the MIKE SHE output. The steps to do this are:
1) File -> New -> File
2) MIKE Zero -> MIKE Zero Toolbox
3) Statistics -> TxStat and select further options from there
Alternatively, we developed a tool that allows you to do other types of statistics. You could also choose to have a higher resolution topo map for the processing. You can learn more about this tool at
http://www.lago-consulting.com/hydroperiod_from_microtopography.html