disabling the active_checks on your service result in nagios doing nothing, and that's normal ^^ (in clear, you're telling nagios that it shouldn't do the service checks :)). (I said to disable them on your hosts; but as they were already disabled...).
Anyway, you're problem is quite weird; getting normal latency for 15 hours (8-9 sec is perfectly normal for such an installation) and then the latency increasing that much is not something I would have expected.
In the meantime, you could read nagios.sourceforge.net/docs/2_0/tuning.html ; this may (or probably not) help you.
And to finish by not really solving directly your problem (sorry :)), I had the "same" problem:
we had 4000 services on one server; although the load on the cpus was not too much (wasn't low either :)), we had a latency of around 12min, and increasing for "each" test we added.
I did some graphs showing the increase of latency relative to the number of services, and we could see that it's increasing exponentially ... which is not a good thing.
In the end, we concluded that the latency is a combination of a software limitation with a hardware limitation:
the better your CPUs are, the further the "acceptable limit" for latency is... but even with a server that was set up far above the requirements of nagios, we still observed a limitation, probably due to the way nagios is coded...
So, to solve once and for all (or not...) the problem, we decided to split our server into 3 servers.
They are on the same machine as before, as the CPUs are capable of handling it.
We created 3 accounts (nagios, nagios2, nagios3), each having access to 2 CPUs. These 3 servers are totally independant (I advise you to do the same; I tried to install the 3 on the same nagios install => it took me a while to get it working, and the performances were really bad).
The result is a very low latency on each server, a better repartition (like: nagios3 for networking monitoring; nagios2 for databases and nagios for the rest), and a crossed monitoring (each nagios is supervising the others :)).
Although the only limitation is that, overall, we use more ressources than before (more disk use, more cpu use, more ram use), but that's a fair tradeoff in the end
Sorry if this doesn't directly answer your problem, but I thought that might give you some ideas
edit: OMG! there are too many smileys; sorry!