You may be right that the nukes aren't fired through the same guns, as far as I know it's everyone's best guess at the moment, although i tend to agree with Snagger on his assessment.
However, having regular nuclear based armaments wouldn't give away the position of a Battlestar, as you yourself said, the Cylons can only detect them once they are open to space. The only reason they would be open to space would be if they were being fired, in which case the Cylons already know the Battlestar is there or the Battlestar is getting the first shot in, leaving the Cylons with not enough time to react.
If they were fired through different guns, they would still have to be opened to space before being fired or they would blow a hole through their hull
So I would say both theories are plausible.