The use of the word "poppet" as a term of endearment or address to a young girl is somewhat at odds with its use to refer to a doll made to represent a particular person for use in various rituals of witchcraft. Such a poppet is an effigy of the person to be affected, much like the popular conception of a voodoo doll.

Wikipedia states (or stated, when I wrote this) that the term of endearment usage stems from the mystical usage, but I was unable to find any corroboration for this anywhere else, and my reading seems to indicate that the use of "poppet" to refer endearingly to a child predates the witchcraft-related usage.

I was reading the Oxford English Dictionary article on this word, and it appears, from close reading, that the word 'poppet' originated from the post-classical Latin 'pupa', via either middle French, Anglo-Norman, Middle Dutch, or a variety of other different languages. "Several other Romance and Germanic languages also have words denoting variously 'doll', 'baby', 'little girl', some of which are borrowed from the post-classical Latin word, some from the classical Latin word."

'Pupa' means girl or doll, and the oldest recorded usage that the OED has (circa 1390) is a small or dainty person. The small effigy or a person used for witchcraft meaning dates from 1400 or earlier. The doll meaning has uses recorded starting around 1500, and using 'poppet' to mean an idol also started about this time. There is also the meaning of 'puppet', which seems to have originated around 1550. The endearment didn't come into fashion until the end on the 1700s and was/is used especially for young women. Originally it was derogatory, with overtones of an effigy or puppet.

So, the endearment definitely came after the witchcraft meaning, according to the OED, but there is no suggestion that it derived from it - rather the suggestion (taken from a liberal reading of the OED) is that the use as an endearment came from referring to little girls as poppets. The quotes seem to make a gradual transition from using the term poppet as little girl to an endearment:

• 707 J. STEVENS tr. J. de Avila Evening's Intrigue IV, in Spanish Libertines: 224 A Lovely fresh Girl, Doctor. My Formal Areta is but a Painted Poppet to her.
• 1794 J. C. CROSS Brit. Fortitude 28: Come along, my pretty poppet{em}your lover's in safety.
• 1830 M. R. MITFORD Our Village 4th Ser. (1863) 253: The little girl as pretty a curly-headed, rosy-cheeked poppet, as ever was the pet and plaything of a large family.
• 1849 DICKENS David Copperfield (1850) iv. 45: It ain't because I don't love you. Just as well and more, my pretty poppet.