We've never discouraged nudity in ours, and we too aren't shy in our house.
none of mine care about running about naked per se, altho don't do it much now downstairs (yougest 5, eldest 13)....altho 5yr old boy takes great delight in being naked with a certain friend of DD1's who finds it all horrible.......am certain he does it more to annoy rather than the freedom thing nowadays.
we do tell them tho that some people find it uncomfortable so should reserve nakedness for at home only (had a problem with DD1 & 2 with nakedness in public when they were lots smaller{tesco was extremely embarrassing......!!!!})
anyhoo.....now DH and I wander freely upstairs and the kiddies don't bat an eye, altho DD1 at 13 is rather more reserved when in front of her dad or brothers....mainly cos the DS's think it all hilarious about the puberty/developing aspect, and embarrass her!(poor girlie, altho she takes it in good humour luckily, just hides as much as poss to prevent their glee).
I think that all kiddies, if left, will find their own comfort level and you should just go with that.......of course tho, explainations about the natural touching as opposed to 'bad touching' of people should be gently explained so as to not let her get into positions that would be detrimental to her IYGWIM.
have fun tho....naked kiddies can be incredibly funny!