Freed,
This is what I found out a couple years ago similar to your situation. While playing the 4 finger G....:
It was some time later that I realized I was muting just as you mentioned, found out when using this chord for arpeggio. So yes it was/is a bad habit even though it still makes a G chord while muting that note.
For quick change chords and rock songs I mute it anyway like this and that turns into a G5 without the B note:
[IMG]
[/IMG]
Good luck!