I didn't even think about it when I was watching. ButAs much as I loved the Titan returning the favour and tossing that rock at the Shrike, I'm pretty sure they didn't know that the portal weapon wasn't in play anymore, and the last head on attack went catastrophically badly.
"Selective observation" is a hallmark of Star Trek. How did any number of people on board not think, "Hmm, I wonder if there's a pattern to these regular pulses of energy?"
Especially when a pulsar is a really obvious thing to check for. But then again, maybe the ship itself checks for pulsars all the time and so they knew it wasn't that.