That’s a good question! I’m in the same situation: estimated processing time of 6 months when application submitted, but now processing time is 9 months.
I think that, technically, the estimated processing time is based solely on when you submitted the application, not on subsequent changes to that time. The website where you check the processing times specifically states that “This processing time is how long we expect it will take us to process an application
if we receive it today.” Also, this post agrees that increased processing times do not apply retroactively:
https://www.canadavisa.com/canada-immigration-discussion-board/threads/october-2024-citizenship-applications.857730/post-11024651
However, I wouldn’t be surprised if applications that were submitted months ago are also being affected by the same factors that are now causing processing times to get longer, such as an increase in applications and/or staff reductions at IRCC:
https://www.cbc.ca/news/canada/ottawa/ircc-immigration-citizenship-canada-job-cuts-1.7436881