Deleting all the lots in the program files lot bin when installing clean templates would cause this kind of problem, but a re-install would fix that.
I imagine playing merged neighbourhoods might also result in weirdness.
Also, there were like FIFTY Secret Society members, even with nodormieregen and nossrespawn. *Sigh* I'd assume this is normal game behaviour, as well. Does EAxis even care about the welfare of their opponents' computers?
The number of SS members is equal to whatever you've set "intProp maxNumOfVisitingSims" to.