IIRC, there were at least three Son’a cruisers in the film.
Two cruisers, one command ship, and the collector thingamabob. At least the last was specifically built by the Son'a, not pilfered from original stock on Ba'ku.
But the Ba'ku got from their original home to the metaphasic planet somehow. I wouldn't wonder a bit if Rua'fo's command ship were the original vessel they used. But given the status of the species as technomages of some sort, once the Son'a got their mini-empire thing going, they could build more stuff at will.
I mentioned this is another thread... in "The Chase", the Yridian ship is destroyed in a single phaser shot. Worf said phasers were not powerful enough to do that, so why did that happen?
I suspect it's this secret agent thing. The Yridians trade in information. Everybody would wish to rob them. So they have James Bond level self-destruct systems in their ships to prevent boarding and capture.
Ferengi starships in TNG are shown to be on par with Starfleet ships. So why did we not encounter any in DS9? One would think the Nagus would travel in a top of the line Ferengi ship.
And he probably is - those little bugshuttles are quoted with very high speed in "Little Green Men", and probably represent the sharp edge of Ferengi excellence. The big ships are just bigger, which doesn't mean flashier - a pop star today might prefer a stretched limo to a regular, but wouldn't arrive in a semi truck or a tank. Usually.
Timo Saloniemi