[quote=@Necroes]
There's a difference between using a psychic attack, which just uses warp energy, and sending out a telepathic homing beacon. Yes, a psyker can notice another psyker using warp energy. However, it's generally not something you can do through multiple layers of hull without actively looking for it. Chances are, the two head psykers on board would be so focused on the battle they're in they wouldn't just be randomly scanning the ship for other warp users, seemingly without cause.

But, a foreign, chaos-tainted, and far less experienced psyker actively scanning the minds of others on the crew over an extended period of time? Astropaths are masters of telepathy, and they would be actively looking for telepathic assault from enemy agents. That is, almost literally, their job description.

So, yea, far more likely the glowing beacon is going to get picked up on enemy radar than the single, random blip among a background of bigger blips.
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However.

The ship we're on is a tiny little crap boat.
Far from all vessels have a navigator, since they're valued resources that don't go everywhere. (One navigator guides several ships during travel, at least if they're good.) And this vessel is probably too small to have a navigator. Or if it has one it is not the best/most powerful one around.
Sure, he/she can still give you the basilisk stare, but will probably not be overly potent at blasting people, like Urgrugg is.

As for astropaths, they usually have to work in choirs to get any good distance on their power, again usually having poorly skilled on smaller vessels compared to large ones.
So i'd say that the astropath would probably be all caught up in the battle. And be about as powerful as Lucius pet psyker. Only focused on something else.
The astropath would pick up the psychic ping, yes. But apart from sending a message to the captain. (As in radio or a runner.) The astropath probably will not alert many of the coming problem.

Since a psychic beacon/sonar can be created for many reasons. Perhaps a new psyker awakened? The ship will not go on full alert because of that.
But they probably will send a team of armsmen for it. To check it out.