If Naboo is the most populated planet of the Chommell sector, then it must be a pretty bare sector. As far as I know, there are one or two city's on the planet, and the one in the movie is smaller than where I grew up. Note that I try to avoid books dating from that time period, as I try hard to avoid it. I'm sure you can guess why. Is the book any good?
It wasn't just in the last century that Corellia and Duro were hugely powerful; they were two of the founding systems of the Republic when the loose conglomeration of trade alliances it came from was attacked by the remnants of Xim's Empire. Corellia has always insanely powerful, (I'd call it the overall most powerful system in the Galaxy), and if Naboo and the Chommel Sector get one seat, Corellia should get twenty.
The Chommell sector was relatively small and of low population, yes. Furthermore, of the settled systems in the astrographical Chommell sector, only a very small percentage were actually in the Republic: most were dependencies of some kind. There's also Naboo's economic weight to consider: as an exporter of plasma and high-energy products, it was the only Chommell world likely to be known by anybody else in the galaxy in the final century of the Republic - and that was before Palpatine's rise to fame, and before the blockade.
Darth Plagueis is generally regarded to be one of the better EU books. It filled in canonical gaps and told a pretty interesting story. Ever since the canonical nuke that Lucasfilm dropped a few weeks ago, it's not clear whether those canonical gaps actually matter, but the story's still all right.
---
The reason I said "final century of the Republic" is because Chommell sector in general and Naboo specifically were still pretty much no-name areas of the galaxy until the energy boom at that time.
Darth Plagueis described a state of affairs that didn't really apply to Rim politics before then.
The "final century" comment didn't refer to the situation with Corellia and Duro, which were founding members of the Republic and retained their Senate seats throughout that body's existence. When the Republic's government was reformed a thousand years before the Clone Wars, many old Senate posts were consolidated as the galaxy was reorganized into a network of 1,024 larger sectors to cut down on the number of representatives in the Senate. Corellia and Duro were some of the exceptions to the rule there.