But...
Not that I'm trying to say Star Trek was real or resolved this issue in any way, but didn't the star ship have navigational deflectors to create a field around the ship which kept things like hydrogen away from the ship itself whilst it was traveling through space? Effectively putting it in some kind of 'happy bubble' for travel. It was a big enough thing in the show that when the navigational deflector was down they couldn't travel.
"The navigational deflector (also called the deflector dish, the deflector array or the nav deflector) is a component of many starships, and is used to deflect space debris, asteroids, microscopic particles and other objects that might collide with the ship. At warp speed the deflector is virtually indispensable for most starships as even the most minute particle can cause serious damage to a ship when it is traveling at superluminal velocities."
Potentially Star Trek still covers it's behind, as hydrogren still falls into the category of "....even the most minute particle...."