I'm more worried about wind than water, it rains buckets down here pretty much every afternoon in the summer, it's not uncommon to get a 5 inch downpour in under an hour.
Yeah I have those pipes coming out of my roof, there's nothing you can do to them for a hurricane right?
A well installed roof will do fine with a ton of rain before sustained wind is in play. It doesn't have to be shingle tearing wind but just enough to get the water pushed under the flashing.
Unless the hvac and water heater pipes were sealed underneath the collar as well as on top there's a good chance for wind driven rain that will get in but it won't be a ton. If it's not caught over several days is what will produce pain in the ass interior damage.
Now the 1.5",2" and 3" pvc pipes that go through the roof usually are installed with a pipe boot that uses a rubber ring to squeeze the pipe (they are here anyway) and this ring cracks and fails at about 8 years. Most of these leak so slowly during a normal rain you never know it. Just check when it start raining to see if water is running down the outside of the pipe and if so tie a towel around it.