As of Indigo version 2.0.106, a new option has been added that allows your session to automatically filter out all Null (0x00) bytes.  

The latest version of Indigo can be downloaded using the link below:
http://www.shadeblue.com/indigo-download

In the Session Properties dialog, on the Formatting tab, a new option "Filter Out <Null> (0x00) bytes" is available.  If this option is checked, then all Null bytes will automatically be stripped out of incoming data.