The narration you quoted is found in a lesser known Hadith book called Mussanaf Ibn Abi Shaybah. First of all, this narration is not a statement of Prophet Muhammad (Sallallahu'alayhiwassalam). This is a statement of one of the Taba'in. Secondly, the analysis of the Arabic text of the narration itself clearly suggests that these girls were menstruating. It is very important to note that girls used to reach maturity at a very early stage during the ancient times.

Imam Shaf'i said: “I saw many women in Yemen at the age of nine reaching the age of puberty.”[40] He also said: “I saw in Sana'a a grandmother who was a girl the age of twenty-one years. Her daughter reached puberty at the age of nine and gave birth at the age of ten. The daughter of that girl also reached puberty at the age of nine and gave birth at the age of ten.”

The Arabic text of the narration states "There is nothing wrong with performing the sexual act upon her without observing Istibra."

What does Istibra mean?

According to Islamweb.net, Istibra means the following:-

Istibra’a, i.e. after she gives birth if she is pregnant or observes a waiting period of three menses according to one view of the scholars, or one menses according to another view

It is very important to note that the narration itself does not say, "There is nothing wrong with performing the sexual act upon her without observing Haydh (menstruation)" rather the narration says, "there is nothing wrong with performing the sexual act upon her without observing Istibra (i.e. without observing menstruation cycles)"

WikiSource Suggests:-

ISTIBRA'. The purification of the womb. The period of probation, of one menses, to be observed after the purchase of a female slave (or in the case of a virgin under age), the period of one month before she is taken to her master's bed.

Here is how AlMaany Has defined this word:-

اِستبراء: (اسم) مصدر استبرأَ/ استبرأَ من (الفقه) تحرٍّ للتأكّد من خروج النجاسة عن جسم المكلف استكمالاً لطهارة البدن المشروطة في بعض العبادات (الفقه) تورّع بترك ما لا بأس به حذرًا ممّا به بأس، وبُعْدٌ عن كل ما به شبهة اِستبرأَ : (فعل) استبرأَ / استبرأَ من يستبرئ ، استِبراءً ، فهو مُستبرِئ ، والمفعول مُستبرَأ استبرأتِ المرأةُ رحمَها : انتظرتْ حتى تحيض حَيْضة ثم تطهر لتتبين براءتها من الحَمل

Hence, the Arabic word استبراء means to purify one'self from menses, as its root word is برئ and this denotes that the slave girls in question were menstruating (i.e. they were mature) and this is because girls used to reach the age of maturity at a very young age in the ancient times. This proves that the girls in the question were mature, as it is not possible for a prepubescent girl to menstruate or observe Istibra!

The other narrations that surrounds the narration in the question also clarify this matter!

This is what a narration in the same chapter says:-

Qutadah narrated:- He used to hate touching or fondling (the slave girl) until or unless she has done istibrah (i.e. purified herself from menses) [Mussanaf Ibn Abi Shayba, 16908].

Conclusion This narration does not say at all that Islam allows to have intimate relations with prepubescent girls. In fact, these narrations actually prove that girls used to reach maturity at a very young age and menstruate at a very young age in the ancient times.