A.F.
My daughter is 2 1/2 and she doesn't bite her nails but she plays with her fingers and puts them in her mouth when she's going to sleep.
Someone told me when I was weening her to remember that its a very sensory experience that they are giving up, and not to be surprised if she takes other comfort behaviors. And I saw it happen, she had no comfort habits before she was weened and now she has several. So I think its part of their development.
I can also say from the biology perspective it may actually be good to have some of these habits some see as not being clean. In the last fifty years autoimmune disease have increased just as other diseases in western countries have declined, where in third world countries they have diseases we used to have, but little in the way of autoimmune diseases and allergies. Its kinda startling if you look at the evidence. This is not to say encourage your kid to get sick, but I am convinced that especially in a first world country where we have eliminated things like polio and small pox, its actually very good for them to be involved with dirt and to get sick with the usual round of things they can get. It helps their immune system develop in a way it couldn't develop otherwise. If you want to read more research the hygiene hypothesis.
And all that being said I think its impossible not to want your kid to be clean, we wash hands all the time, and bathe our dd daily. I just try to be ok with her playing in the dirt and putting her fingers in her mouth.