WebOffice 10 R3 supports map documents with multiple data frames. As ArcGIS Sever is a powerful fully scalable server technology, providing a highly available and fast application system will consume a lot of memory and CPU resources (high count of SOC processes on the server). You can reduce the overall count of SOC processes significantly by putting multiple data frames in one map document.
The tradeoff for map documents with multiple data frames is basically increased complexity when managing the map document.
Note: If you use an mxd document with multiple data frames it is recommended to set the Server object instance count to the value 2 at least. This will increase performance of project startup when opening a project in the browser.

Setting Minimum number of instances to value 2
You should think about using multiple data frames if the data frames use different data sources and if you need high availability. If one data source link for a data frame is broken this may affect the other data frames then because all data frames are served within one SOC process on the GIS Server.