N.,
I would not worry too much about it affecting her nutrition. Bottle-fed babies tend to eat more than they need to because the bottle flows more readily anyway. If she's hungry, she'll eat.
As for paci vs hand...I feel it is a good thing that she has learned to soothe herself. My 5 1/2 month-old, also re-discovered her thumbs/hands at about 10 weeks old. (She was sucking her thumb during one of her ultrasounds, but did not do it during the first two months after her birth.) While it doesn't bother me, my husband HATES the habit and always pushes her hand away. My baby is undaunted though, and just goes right back to it.
For me, the issue lies in "the long-run". "If allowed to suck her thumbs/hands now, will she stop at an appropriate time in the future, or will she be 14+, in high-school, talking about boyfriends and sex, while sucking on her bulbous thumb in class!" (This is not a made-up situation!! I actually witnessed this!)
Anyway, what we do with our little doll is give her the paci whenever possible. We don't stress about her sucking her thumb/hand (Not even my husband) but we try to minimize it by offering the paci also. This way, hopefully, it won't be a long-term habit. She does take it, but whenever she needs some soothing she goes to her ready hand since we fail to read her mind.
Hope this helps. Congratulations on your little one and good luck to you!
-I.