We kept it kinda vague on purpose, but unofficially (as the person who wrote M3 and the sabotage plotline ) it's a Simon who was aboard as a medic who was the one who planted the bomb.
Question: How did the crew find out he was a Cylon, and not just a human turncoat? The best thing I can think of is that it happened the same way as in "Razor," and there were one or more Simons (or whichever model) in the boarding parties on the Heavy Raiders, but I'm assuming that if you aren't a distractible flailing idiot like me, it's possible to make it through the mission without the ship being boarded, which rules that out. And no mention is made of the gas giant's electronic interference being particularly bad for Cylons, like Ragnar's, so they didn't figure it out the way Adama did.
And, getting a bit further afield, I don't think the cylon transponders were intended for ships that were supposed to slip past, but were just to announce the presence of a Cylon agent. Galactica
only made it though the miniseries because Tyrol's deck crew went above and beyond in restoring the museum ships, and Starbuck got in a fight with Tigh so she was in the brig rather than with the rest of the good pilots in the main squadron that got wiped out in the Mark VIIs. If Galactica
hadn't had those antique fighters ready to go, or if they were all being piloted by bench-warmers, two raiders with nukes would've been more than enough to take down the ship.
Of course, figuring out why Doral or Boomer or whoever stuck the thing right in the middle of the DRADIS console in the CIC rather than hide it in a less conspicuous location, like literally any other place on the ship, is beyond even my considerable skill at fanwankery.