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 versions of Indigo, including BETA version can be accessed using the link below:
http://shadeblue.com/products/indigo/download.aspx

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.