The incidence of hypospadias has been calculated at 1 in 300 live male births. In the US, about 6000 boys are born each year. Familial tendencies indicate some genetic factors due to the fact that fathers with hypospadias have an 8% chance of passing the defect on to each male child he fathers. Also, 14% of male siblings are affected. This condition is more common in whites than blacks.
The most common associated anomalies would include undescended testes and inguinal hernia.
Other less common associated anomalies include upper urinary tract defects. It is recommended that all patients with hypospadias have their upper urinary tracts evaluated to some degree.
In reguards to intersex. Hypospadias is thought to be a form of intersex. Certainly the diagnosis of classic intersex must be ruled-out in cases of severe hypospadias, especially those with associated undescended testes.
Your last question I can only respond to with the comment that there is no know study or research to support the statement that homosexuality and hypospadias are linked in any way.