The matter is broad in scope. She may say the words that suit her (i.e., the feminine form) and say Ana amatuka (I am Your female slave), or she may use the wording of the du’a that is narrated, because it is describing the person who is speaking, and may apply to both male and female. 

Shaykh al-Islam Ibn Taymiyah was asked about a woman who heard in the hadeeth “Allahumma innee ‘abduka wa’bnu ‘abdika, nasiyati bi yadika (O Allah, I am Your slave, son of Your slave, my forelock is in Your hand)” and she persisted in using this wording. It was said to her: Say “Allahumma innee ‘amatuka bint amatika … (O Allah, I am Your female slave, daughter of Your female slave…)” but she insisted on reciting it in the wording that she had been using. Was she right or not? 

He replied: 

Rather she should say “Allahumma inni amatuka bint ‘abdika ibn amatika (O Allah, I am Your female slave, daughter of Your (male) slave, son of Your female slave). This is more appropriate. But if she says ‘abduka ibn ‘abdika, then it is acceptable in Arabic usage, like the word zawj (spouse) which may be applied to both male and female. End quote. 

Majmoo’ Fatawa Ibn Taymiyah (2/177). 

Ibn Hajar al-Haythami (may Allah have mercy on him) said in al-Fatawa al-Kubra (5/342): A woman may say in sayyid al-istighfar and similar du’as: Wa ana amatuka bint amatika (I am Your female slave daughter of Your female slave) or bint ‘abdika (daughter of your male slave). But if she says ana ‘abduka (lit. I am Your (male) slave), this is acceptable in Arabic usage, like the word shakhs (person) which may be used for both male and female. End quote. 

Al-Shaykh ‘Abd al-‘Azeez ibn Baz (may Allah have mercy on him) was asked about this and he replied: The matter is broad in scope, insha Allah, but it is better for her to say Allahumma inni amatuka wa’bnatu ‘abdika wa’bnatu amatika (O Allah, I am Your female slave, daughter of Your male slave, daughter of Your female slave), and so on. This is more appropriate and more befitting for her. But if she says the wording that is narrated in the hadeeth, it does not matter insha Allah, because although she is amah she is also ‘abd, one of the slaves of Allah (‘ibaad Allah). End quote. 

Majmoo’ Fatawa Ibn Baz (6/76). 

And Allah knows best.