Those are not stupid questions at all. In fact you have touched on some very contreversial subjects. I'll give you my opinions.
1. Why are some carbs ok and others not? Like why are wholewheat carbs ok but processed carbs are not?
Fibrous veg are high in nutrients and fibre while low in calories. Eat all you want, they will fill you up. Beyond that, wholewheat, beans and tubers are high carbs and high calorie and should be managed. All are better than highly refined grains due to their higher nutrient levels.
2. What's the deal with glycaemic index? Is that important for fat loss?
Slow carbs have less of an effect on insulin but overall it may not be that big a deal. Less processed is always better but GI may not be as important as previously thought.
3. If she was to limit her carbs, what's a realistic figure to try and hit? Bearing in mind she's a sedentary 22 year old.
Look for my link to Marks daily Apple. He breaks it down nicely. Under 100-130 carbs, the body goes ketogenic and burns fat. Maintenance is slightly higher. 200-300 is OK for gaining while over 300 is for getting fat. I know my numbers are ballpark but the article goes into more detail.
Edit: http://www.marksdailyapple.com/the-prim ... continuum/
4. What's the deal with protein being thermogenic? Can that factor in weight loss?
The effect is small but it is real. Protein and fat satisfy hunger more than carbs. This is a much bigger effect.
5. Are there any ill effects from restricting carbs?
Having some carbs makes eating more enjoyable but many people eat no carbs and get by very well. I think it's extreme and boring to live off pemmican all the time but it's possible.
Here's are 2 great zero carb blogs.
Zero carb should not be confused with low-carb. It is more extreme.