She will get used to it... also after you clean her eyes give her a treat and praise so she knows she has done well and to get used to it...
I think they are brown and this is normal... Samy does not have much but i am assuming this is because he is still a puppy... my friend's female yorkie has plenty and they are dark brown but the owner does not clean her every day, maybe a couple of times a week... I make sure to do it every day and it happens to be in the same time of the day so he is now actually looking forward to it and gets excited when i pull out the wet napkins
he still bites on them but loves the treat