If i have sex with my wife while she is pregnant is it physically different in any way?

Not really: The baby is too far up and well-protected to be impacted in any way by vaginal sex, so that should be of no concern. As the pregnancy gets farther along, many couples find the missionary position to be uncomfortable simply due to the side of the growing belly, so alternate positioning on the side, from behind or with the woman on top are often preferred. Lady's choice, generally speaking.