I guess it depends on the program.. typically you can just drag the application's folder, not to be confused with the "Applications" folder, to the trash can and delete it and bam that application is deleted. Now preferences, etc is a different matter, but you don't have to worry about that unless you are worried about disk space and then we explain how to delete that info later.
And yes for some reason OS X does it's maintenance scripts around 3 or 4 in the morning.. I can't remember which.. it also does maintenance on startup, that's why it takes a little longer than other platforms, but then it makes up for not having the problems other platforms have so in the long run.. you save A LOT of time because of it.
You can download programs like Onyx, which I use, that allows you to execute those maintenance scripts whenever you feel like it. Or you can go in and edit the cron jobs to execute those maintenance scripts at a different hour.
There are quite a lot of things you can do and whenever you have questions you are in the right place... there will be someone that can answer
Cheers!