Yes, 40K is pretty wild, and it's hard to scale or measure it up. But even in the most gaping maws of violent chaos, certain things must be respected, and logic prevails.
Even a 10 percent of failure would mean that in average a fleet will only survive so many jumps before being wasted to oblivion. Making hastily and bad maths you have that after only 10 jumps a fleet would be down to less than it's 35%. That's it, having a fleet of 100 ships would left you with less than 35 after only 10 jumps.
By the time of the 30th jump you will have less than 5 ships. And remember we are talking about a mere 10%.
If we rise up the number to the insane 40% chance for our 100 ships fleet, then by the time of the 10th jump you would have around 0,6 ships... which unless the ship is on a "dry dock" being constructed, is kinda a bad thing to be in.
Or to put it on another way, travelling with a 40% chance of being devoured by oblivion every single time you do it will land your ass in oblivionland in less than 3 trips for most people AND ships. Which is kinda of the other side of this.
Ships, we have ships plenty, and thank the Emprah for the oncoming Battlefleet Gothic pc game, but enough of that. How many ships do we have that are ancient? Like really fucking ancient? A lot, if not most of them. That would be a really hard thing to accomplish on a world were 4 out of 10 are ships get lost forever in their maiden voyages, and the rest are lost in mere three trips on average. Wouldn't you think?
So, either that number is a lie or the fact that you have even a single ship that is older than dust is a lie, the two of them cannot coexist. I know plenty of lore of ancient ships, don't know any of that high rate of failure to travel, hence I'm sticking with the it's fake or a mistake hypothesis. You people are free to take your pick.
PD: I won't deny there's situations were the chances of making a successful jump may slip into the realms of "no fucking way we're gonna make it" as the plot requires (or even things far worst like arriving before departing), however that would be especial circumstances, not the norm.