Ok here is my routine. Yes, if she whines RIGHT WHEN you put her in her crate at night (and she has Poo'd and Pee'd, and you know she is comfortable) yes, then ignore her, but I would NOT recommend getting her up in the middle of the night. I would think that would be instilling bad habits if you want her to sleep through the night eventually.
My 3.5 month old cried the first few nights (right away after putting him in the crate) for 25 min. the first night, 10 the second and about 2 min. the 3rd night, but from then on.......slept AT LEAST until 5 am.........and now sleeps until we get him up (7am or later on the weekends).
Did you say how old this puppy is? Was she getting Pee Pad trained where you got her? I brought my puppy out every 30 min. NO FAIL and still bring him out every 30-45 min and he goes ALMOST every time. You say she isn't drinking or eating much?? How about getting a BULLY STICK or TAIL and let her chew on that to get her thirsty......I guess the more she drinks the more chances at this point to teach her OUTSIDE POTTY??
