I haven't seen anything in FS canon to suggest any sort of number of FS1 ships. As for not seeing very many of these ships, You're not everywhere at once during the events of FS1 and FS2, so none of us can see the whole picture (if that even means anything).
Whether it's hundreds or dozens, I honestly have no idea.
But considering the large size of Terran and vasudan destroyers (and the fact that there are only 13 terran fleets and 13 vasudan battle groups) there can't have been more than a few dozen GTVA destroyers at the start of FS2. There couldn't have been more than 100 or so destroyers total.
Remember, during the NTF Rebellion, destroying ONE cruiser and ONE destroyer constituted a major victory. For that to be so, capital ships would have to be relatively rare.