Also, the Redjac entity hacked into the computer system to exploit it as a hideout, a rare infiltration in that the act did not grant it complete access to the entire system or allow it to control all of the ship's functions.
More conventionally, the Maquis hacked into USS Malinche
and USS Defiant
in "For the Uniform". And various clever enemy operatives performed partial hacks of DS9 or Defiant
systems in that show, including Klingons, Mirror Universe visitors, Garak and our heroes-turned-resistance-fighters during the Dominion occupation.
Only Adama's stubbornness kept Galactica being modernized too
I thought that was more due to Galactica
being a museum piece that wasn't intended to be used in action ever again?