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There are certainly renegade navigator houses, as found in The Navis Primer. You can also kidnap one. And there are psykers who can double up as a makeshift navigator.
Pirate is a massive category in 40k. It can range from navy deserters, to scroungers, all the way up to aeldari/human adventurers or chaos marine warbands. Their capabilities also vary wildly.
In short, as has already been somewhat adequately explained: Navis houses are extremely powerful and extremely corrupt, and having a junior navigator fall off the back of the bus to aid someone they're allied to or their pirate servants, isn't a stretch.
The tech-priests have widely different factions, including straight up chaos-aligned ones, and pirates usually contract the services of heretek mercenaries. What you have to get is that the adeptus mechanicus is ALLIED to the Imperium, they are in no way identical to the other adepta in their beliefs, and in the case of the oldest tech-priests, no longer even really human. Their alliances can vary in the extreme.
Then birth of Slaanesh happened, and the warp storms and so on, which made warp travel almost impossible.
Only after that, we have the unification wars, and the birth of IoM, and the Astronomican.
So in the "modern" age, navigators use Astronomican as a reference point for long range navigation, but in theory, the short range navigation should still be possible even without them, just with much higher probability of bad results.
Also, both navigators and tech priests can be corrupted by chaos, and they too can have loose morals, and cooperate with pirates, or find justifications why that is OK.
For example, on Footfall, we can meet a priest who was serving on a pirate ship. If ecclesiarchy can be convinced that that's "OK", so could others too.
It is THEIR domain, afterall.
The strict lifestyles the navigators are meant to follow all while being disdained and ostracized can also push some of the younger ones to become outlaws. Some pirate crews are mutants who just wouldn't be accepted by anyone but each other.