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.