Adding NULL packet removal to H2 probably wouldn't be that hard. PID removal support in order to remove sub-channels would be a bit more difficult as several tables would have to be updated, but it is doable.
In theory, converting to mpeg should remove the NULL packets and sub channels( I haven't looked at that part of the code). But going through three translation tools to remove NULL packets and PIDS is likely to be a frustrating experience because all of these "free" tools have lots of bugs.
We should just ad the ability to remove NULLs and PIDs to H2, don't you agree?
For myself, I would just use TSReader ($99). You just load in the TS file, select the Program you want to keep and select to remove the NULL packets. But then, I already own a copy and use it for other things besides NULL and PID stripping.