Yeah. I still dont see the navigator issue. Or at least whats been trying to be presented as an issue.
Navigators are rare. But they are also the bottleneck of warp travel.
So they are going to be present whenever there are warp travel going on.

Is it established in lore that the Imperium actually HAS lots of ships around which don’t have Navigators, or is it just that it COULD do? Because the perfectly rational reason for why there are always the number of Navigators they need is because they don’t bother building more ships than they can reliably supply with Navigators! Over tens of thousands of years the rate of ship production has adjusted to approximately meet the rate of Navigator production!
But i think Avaris is in to something here.
This is honestly rather logical. Likely the Navigator production is moderatly predictable.
While the ship production is is easy to control. Or no. This is 40k. If they really wanted a ton of navigator babies they could likely get them.
Issue is more i think that the navigator houses has a stranglehold on warp travel. And so they control their numbers,
to ensure that they are only -just- enough to barely cover the needs of the Imperium.