Some responses out of my feeble, allnighter brain:
1) The Caranthians (= refugees) are from another plane of existence, and their enemies are very solidly back in that dimension and will not be able to chase them; the elves saw to that. Very few of the Caranthians are sailors - most of them died in the wars trying to defend their homeland from being overrun. What they are, happily enough for the Vinarians, are maritime trade workers: shipbuilders, ropemakers, chandlers, longshoremen and the like. They've not been terribly content in inland Vinaria ... and are, by the bye, from a much warmer clime than Vinaria; they'll adjust to the heat better.
2) System is GURPS, which means that with few exceptions, cannon fire trumps magic. Weather control spells work quite well in helping ships along, but there's no combat spell in the book that'll outrange a culverin.
3) There's a lot of timber on the mainland, just a few miles away; the Vinarians are counting heavily on that timber, because it takes a LOT of wood to build a warship. It's barely-inhabited jungle, with unknown nasties and haunted ruins in there. They're expecting such troubles, are unsure they want to tie down that many soldiers there quite yet (and that land is claimed by a nearby nation) and are contemplating just buying the timber from local lands.
4) The problem with building a fleet ahead of time is simply in the size of the Gate; it's 21' x 12' and around 1600 miles away, which in Create Gate terms is freaking staggering - making it larger was just not going to happen, and making it THAT large was a terrible risk. You can push the hull of a dismasted schooner of not much more than 70 tons through that, about. It's dandy for keelboats and flatboats, though, and they're what's carrying cargo traffic both ways.
5) Pirates not so much of a problem - the PCs in the middle of all this went on an embassy to the Pirate Isles ahead of time to buy them off and hire a couple of them for mercenary naval patrols for a year. Still, there'll be renegades.
6) Huh. D'ya know, I didn't think of the problems they might have with pushing the five schooners they DID get through the Gate with such a rapid change of temperature. Certainly their wizards could have made the transition less harsh, but they likely wouldn't have thought of it.