You don't think that a) me bending up those pins, b) a damaged cable or c) a potentially faulty usb to sata cable could have caused any damage causing the lack of hdmi audio do you?
What do you want me to say? I cannot judge whether the ports of your RPi are still functioning properly.
People should be aware that all ports of any Raspberry Pi should be treated gently.
They are not the exhaust pipes connected to a typical car's engine block.