Well, besides having dark hair, Bay is pretty fair skinned as well. Gosh, she would make a good Snow White.
Anyway, I always wondered as well why Regina didn't think it was weird her daughter had red hair and didn't look like a latina at all. But later it is revealed that she did found out when Daphne was three, but just didn't say anything to anyone.
And in the end, the possibility of having your child switched is so low, that it probably wont cross your mind. She gave birth and took home what she was told was her child - she probably thought it was weird, but genetics can be weird sometimes :)
Like the other person said, genetics are weird. Even if you or your spouse don't have red hair or blue/green eyes, your baby still can. Those traits are technically considered mutations, so they can happen to anyone, and it can appear if someone in your lineage had them in the last few generations. She probably already knew this, or someone reassured her when she asked.
I have dark skin and dark eyes,thanks to my mother's Sri Lankan heritage but my dad is Scottish, and him and his 3 sisters are all red heads. (my cousins are all blonde/red hair and blue eyes.) You'd never know it, but because my boyfriend's heritage is Scottish too, the chances of me having a red head child are quite high. It would look like Regina and Daphne. It could happen.
Not necessarily considering Bay is mostly white and she is ridiculously pale. People's complexions change a lot as they get older too. A lot of Latino people are as light as Caucasian people and you might not know unless you asked or it came up in conversation.
Also Bay is not fully Puerto Rican. Angelo was French so he could have had a fair haired and fair eyed child. But to really answer the question... Regina didn't question it because she knew she hadn't been with anyone but Angelo so there was no question in her mind that daphne was her daughter.