Plagueis was still alive and Palpatine was Senator when the crew of the Katana fleet were infected and disappeared into hyperspace, not to reemerge until the Thrawn Campaign. It seems like such a devastating loss to the Republic might have likely been engineered by the Order of the Sith Lords. Instead of being dispersed to the judicial forces those 200 dreadnoughts were to be retained as a cohesive fighting force. If the Katana fleet had not been eliminated it could have helped to prevent the Republic from spiraling into chaos during its waning years. By eliminating the Katana Fleet fleet the Sith would also highlight the corruption and inefficiency of the Republic. Powerful guilds and corporations like the Trade Federation and Banking Clans might also conclude that the Republic simply wasn't capable of defending their business interests and take matters into their own hands, either by creating their own armed forces or accelerating already existing military buildups.