Subhadra and Yogamaya are two separate sisters of Shri Krishna. Of them, Subhadra was the daughter of Vasudeva and Rohini. She was not Yogamaya. On the other hand, Yogamaya, the daughter of Nanda is Shri Krishna’s other sister. She is Devi Ekanamśā or Devi Vindhyavasini. Both sisters have been described in the Harivamsa.
Subhadra
Subhadra has been described as the daughter of Rohini and Vasudeva, much younger to Balarama:
O king, the daughter of Bahlika and a lady from the Puru dynasty, named Rohini, is the first and most beloved wife of Vasudeva. He begot of her, his eldest son Rama (Balarama), Sarana, Shatha, Durdama, Damana, Shvabhra, Pindaraka, and Ushinara. O descendant of Kuru, Rohini also had a daughter by the name of Chitra, who is also renowned by the name of Subhadra, the wife of Arjuna.
Harivamsa Parva, Chapter 35, verses 4-6
In the next verse, the birth of Abhimanyu from Subhadra and Arjuna has also been affirmed.
Ekanamśa
From the story of Ekānamśā below, we can see that she is still unmarried, and the incarnation of Goddess (as she herself says in Devi Mahatmyam), very different from Subhadra.
The story in brief:
In the midnight, at the auspicious time of abhijit, Devaki, gave birth to Vishnu and Yashoda gave birth to a girl. Unknown to Yashoda, Vasudeva kept the boy with her and carried the girl to Devaki’s bed.
Vishnu Parva, Chapter 4, verses 14 & 26
When Kamsa is about to kill the baby:
Suddenly, she gave up the body of the new-born. With disheveled hair, adorned with celestial garlands and pastes, she addressed Kamsa. All her limbs were shining with garlands. She was adorned with a dazzling crown. The goddess remained a kanya forever. She was praised by all deva-s. In the night engulfed by darkness, she dazzled with her Bhutaganas. She danced, laughed and manifested with opposites. this Goddess is born from a portion of Prajapati (brahmA). Hence she is Ekānamśā - one and without having any portion (division) (with brahma). The Yogakanya appeared for the protection of keshava.
-Vishnu Parva Chapter 4, verses 37-47
As per Narada, this is the same goddess who lives on the Vindhya mountain, after killing Shumbha Nishmumha:
That girl of Yashoda, killed the danava-s, Shumbha and Nishumba in the forest, on the mountain of Vindhya. The place in the vindhya mountain is made by her splendour There, the beautiful goddess terrifies her enemies. Worshipped by the devatas the, the Goddess stays there, highly pleased.
-Vishnu Parva chapter 22.52-58
From the above it can be seen that Subhadra is the daughter of Rohini and Vasudeva and is in no way connected to or any incarnation the Goddess. On the other hand the Goddess Ekānamśā, daughter of Nanda and Yashoda, resides on the Vindhya mountains (Vindhyavasini) being worshipped by the devatas and is unmarried. They’re two separate sisters of Shri Krishna.
As regards your doubt on Manusmriti, we can see in the Mahabharata many people did not follow it. Also Nara is not Lord Shiva, he’s very much an incarnation of Lord Vishnu.
