I wouldn't say she's developing unhealthy eating habits. It seems to me two things are going on here. I think she's entered a phase where she's testing you and seeing how much "control" she can wield through whining.
Secondly, I think she's being a typical picky toddler. They all go through several phases of eating only one thing, and nothing at all, even at dinner time. The fact that her snacks are with her all day, probably isn't a good idea.
I think the key is to not let her whining rule you. Give her options of what you think she should eat, and offer puffs as her reward. If you give her two things to choose from, she'll feel a sense of control and though she's not in charge of carrying her snacks around, she may still be more willing to eat it since she chose it. I know it gets boring, but keep lots of stuff you know she'll eat, and let her choose from those things.
Second, my pediatrician told me if you keep putting a good variety of healthy/nutritional foods in front of a kid everyday, and they only pick at it, an amazing thing happens. They do get the nutrition they need and they do get enough. She says kids stomachs are only as big as their fists, so they really only need so much. She also said, with the picky types, it may seem like they're not eating healthy or enough, but she hasn't known any who will let themselves starve. They will eat whatever you give them. The key is to stick to your guns.
My oldest was totally addicted to those Gerber Wagon Wheels and puffs and was nuts for cheerios too. Unfortunately, he'd fill up on those and then not want his regular meals. I think the appeal for him was that they were little and easy to pick up, and crunchy. Nonetheless, I had to do something to get him to eat more than air-filled grain.
To get past this I started making his regular meals more like "crunchy" appetizer/finger food trays so they'd be more appealing. This worked somewhat, because I started to realize he was more of a grazer than a big sit down meal kinda guy.
So instead of breakfast, lunch, dinner, and 1 or 2 snacks in between, I started to make his meals smaller, but space them so instead of two meals and a "snack", he was actually getting 3-4 smaller meals during the day, and then dinner with us at night. If he only picked at his stuff, I at least knew over the entire day, he probably ate enough to equate to at least one meal.
This worked great for us, because we just eventually began to avoid getting into the treat vortex thing altogether. If necessary I would use the puffs to get him to eat if he was in a picky mood. I'd say no puffs until you eat the good stuff! And he'd complain, but do it.
I also started hiding healthy stuff in the things he would eat(check out 2 good cookbooks "Deceptively delicious" and The "Sneaky Chef" both are at most stores and Amazon.com), and most definitely assigned a name to all of the foods using all of his favorite "characters" such as "Dora pancakes" and "Diego links" for sausage..Thomas the Tank steak, and "Tubby-toast" for grilled cheese and "Cars" soup (for Minnestroni) "Brocolli Trees" for brocoli, and my favorite "Oscar-mix" as in Oscar the grouch for spinach. It's amazing what they'll eat if it's named after a buddy.
Here's an example of one day's mini-meals:
Mini-meal 1: 1 Toasted whole grain waffle(crunchy!), 1 turkey sausage link, 1/2 cup of yougurt(on the side, sometimes on top of the waffle), milk.
Mini-meal 2: 1/2 cup of cubed cheese with 3-4 whole wheat crackers(crunchy!) 1 cup fruit Juice.
Lunch: 3 baked/breaded chicken nuggets(crunchy!) 1-2 Breaded and baked cauliflower and broccoli (crunchy!) cup of applesauce, milk.
Mini-meal 3: Graham crackers(crunchy) and cup of milk.
Dinner: What the big people are eating but a small amount and named for sure after some "character" of the day.
Last but not least. If all else fails, I have a friend who is quite the natural when it comes to child psychology. She tells her kids if they don't eat it when they're supposed to, "that's okay". She wraps it up and puts in the fridge and serves it for the kids next meal, even if everyone else is eating something else. If they won't eat it then, she wraps it up and serves it at the meal after that..and so on.
She doesn't let them have a snack in between, and definitely no treats or desserts. She says after one day of this routine, the kids usually eat everything if she puts in front of them the first time around...otherwise she threatens to "wrap it up" and they make themselves eat it..even if they hate it. Now that's something!