Two big reasons to use acrylics are less smell and faster drying. Since you are brushing rather than spraying, smell is much less an issue. If you want matt finish vs gloss, enamel flats do dry pretty fast, like acrylics.
I personally like enamels. But my main reason is compatibility with what I airbrush. But I do find coverage better with enamels than with acrylics when I do brush paint.
For you, I don't think it makes much of a difference except maybe if you want a gloss coat on spars and decorative woodwork, you'd have to wait for the longer drying time. However, no ship kit is an excercise in speedy modeling, so again I don't think it makes that much difference. Drying time even for gloss enamels is a small fraction of the time you'll spend building a 3-master.