They do however most Ha'tak have the same frequency, it is pretty hard to use the same tech to change frequencies. It wasn't practical as I said to storm a Ha'tak at full strength by Force (Of course with the Kull Warriors it was a lot easier) and Anubis had a lot of power behind him even before he made the Kull Warriors.

It was usually a case of trying to batter it down to the point where its life support was ruined and it couldn't fight back to where it was possible to take the ship by force.

Of course, if that isn't possible just blow it up.