Flynn
Regarding your opening post...
(Disclaimer: I don´t have the full rules yet, so what I say now is mostly what passes for common sense)
Having many small ships definitely has the advantage of being able to be in several places at once, which is very useful if the threat in each place is low enough for a small ship to handle it - like, blockade/quarantine duty, customs patrols, anti-piracy patrols and so on, but probably not a full-scale war.
For example, it´s much more economical to stop and search a suspected smuggler with a frigate than with a battleship.
Also, while it may be that a number of smaller ships that are as powerful as one big ship may take longer to build, you can build many of them at the same time for the same money and effort as building one large ship, meaning you will have the first of them available a lot sooner in case you need them, instead of having one half-finished (and useless) large ship.