Problem: HDHomeRun dual tuner has a 100Mbps Ethernet port. Two full 256QAM channels could take more than 100Mbps, making it unusable. This will become the case now Ziggo is moving some of their transponders from 64QAM to 256QAM.
Solution (yes there is one!): use PID filtering. See the response from Silicondust below:
You would not be able to stream 2 full QAM256 channels at the same time. Modern PVR programs like WMC7, MythTV, and EyeTV support what is known as PID filtering, where they tell the HDHomeRun to only stream the specific portions of the channel that correspond to the particular program being watched/recorded.
I'm aware you've got a lot of work to do with a small team, but this one seems quite important because of the move toward 256QAM that Ziggo is implementing.