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Yeah, they are. There are a few dozen "great clans" or Houses of Navigators who self-impose a sort of eugenics programme to maintain the mutation and attempt to improve the overall sensitivity and precision of the typical Navigator's Eye.
Regardless of how they come about, we know there are sufficient Navigators about for there to be competition both within and between houses for prestigious postings, and that being assigned tramp-freighter duty is a sure sign of disfavour from your Clan Lord.

Though some more recent fluff that's gotten way ahead of itself on the grimdark front treats Navigators (the Navigator Gene being a hand-crafted gift from the Emperor himself, remember) as interchangeable components, like fuses, expected to occasionally burn out, regrettably and unreasonably inconveniencing the important people until such time as a replacement can be brought up from stores, which would imply that even more of them exist than the other model does.

Depends on how wealthy the citizen is and his/her value to the empire, members of trading houses have their own ships, the whole infrastructure is held up by trade and tides, i also think that warp accidents happen less with civilian transports as they take safe routes and take less risks while traveling the warp.

 Jehan-reznor wrote:
Depends on how wealthy the citizen is and his/her value to the empire, members of trading houses have their own ships, the whole infrastructure is held up by trade and tides, i also think that warp accidents happen less with civilian transports as they take safe routes and take less risks while traveling the warp.

They also get worse navigators though. The top tier organisations in the Imperium (Astartes, Mechanicus, Inquisition, Ministorum, Adeptus Terra) will hog all the brightest stars the navigator house produces, by virtue of necessity, oaths, position and wealth.
The Administratum, Guard and other Imperial organisations will get the B students.
The civilians will have to make do with the black sheep and dropouts.

Even so, not every warp capable ship will be able to secure a navigator. You can do short jumps along stable routes reasonably safely without them- which is how they managed before navigators. Smaller industrial houses may have deals with larger ones and travel in convoys, lead by one ship with navigator.

For these reasons I reckon warp accidents happen with about the same frequency to civilian traffic- their precautions merely lowering the risk to the military average.