It's noticeable over the years and as well as vs Kent services
The Sydenham stoppers are now timed to take 10 mins from NXG to London Bridge, so 5-6 mins extra on the up vs down. The London Bridge service has just got more and more unattractive.
Service frequency and passenger numbers certainly plays a part in this.
If you are running a train every 10 minutes on a line, you can run it smoothly and even accrue a 5 minute delay without any real impact on onward problems, besides potentially missing a path at a key junction (although the frequency means this is less likely to be a problem)
If you move the frequency up to every 5 minutes, a 5 minute delay causes the service behind to get delayed by a similar amount, and even the one behind that will start getting restrictive signalling. Pathing is more likely to be an issue also. It is not an issue that scales equally; a more frequent railway is a more congested one and delays exponentially increase. Passenger loading is a major element here.
If you run a reduced service with less passengers, dwells can of course be reduced, running times can be increased and performance is generally great - just look at performance in 2020 & 2021!
As a note, the booked timetable may well have been that from New Cross Gate to London Bridge, but the congestion around London Bridge / Bermondsey was notoriously bad with a number of flat crossing and trains weaving all over and there were often delays into London Bridge. Rationalising the layout - and building the Bermondsey dive-under - was a major part of the Thameslink programme.