having Duokan certainly doesn't because nothing of it is running on the CPU when you're in the Kindle GUI (when idling in the Duokan GUI, I can't really tell - though in my experience it doesn't make a difference).
For FBKindle, basically the same applies - but: It is usually started by launchpad. And launchpad *is* running on the device. Though I haven't heard of any complaints, it really depends on how launchpad goes to sleep. After looking in the code, I see it uses select(). I'm not sure I see everything at the first glance, but it seems it uses a 1sec timeout for that select() call, which means that every second it does a syscall. That's at least some overhead - I don't know if it's noticable, however.
Other hacks are usually started by launchpad. It's separate software in most cases and running it will of course need some power.
Screensaver and font hacks will most certainly be negligible. It's just running code against one kind of data vs. other kind of data. Plus minimal overhead upon boot.