First off, if you're concerned about getting bad habits you do not need to use the HUD with the tracking software. You can simply track your stats. For example, if you see that you look at your ring games and see that you are losing money in any position except the blinds, that is a major indication that you are doing something bad from that position.
The HUD is a big help when multi-tabling. If you have six tables up, keeping track of all 48 villains can be rough. So you fall back on the stats.
When I play tournaments I only single table. In tournaments the action will change depending on the stack-to-blinds ratio so the stats I see in the HUD don't mean a lot. In fact, I discovered about a year ago that I did *better* in tournaments when I didn't use a HUD because I paid more attention (I'd get bored and use the stats as a crutch as I did other stuff).
Since then I've stopped paying attention to the HUD, and only use it to see mucked showdown hands. (Seeing those cards is great for seeing how people played and that convenience is almost worth the price of the software alone). I mean, I still have the stats up, I just don't read them unless I want to backup the read I had on someone.
HUD's are also great for keeping track of your reads. That is, you deal with hundreds of different players each week online. When you bump into someone you've played before, it's a big advantage to know how he's already played. You have an instant read without having to relearn how he plays.
Basically, for a good player the tracking software will pay for itself fairly quickly and will teach you about your own play as well as how others play. If you're concerned about learning bad habits, don't use the HUD, or only use it as backup (like I do in tournaments).