Actually, Eder, I get the impression that those things were not simply missiles - they looked like... I dunno, fuel tanks or something. Much too big to be missiles or even capship missiles.
The Waterloo may be too small to house Broadswords, or it might not. What we do know is that it ain't small enough to launch Crossbows (which are, admittedly, a bit smaller). A lot of people complain about Crossbows, but they were fairly capable bombers IMHO (and certainly, no matter what their stats were, they looked just bloody great)... why not use them, and restrict the Broadswords to the Perry base? An alternative solution would be to have a very limited number of Broadswords, and say that they actually dock externally. I'm certain that, given the Broadsword's inter-system capabilities, the ability to dock with capships would not have been forgotten.