I know that changing the personality with a cheat doesn't change anything about the genes for personality that the sims pass on. You have to sync that with the FFS Debugger if you changed something, as far as I know.
But what about the looks? If I change a face with the the Simblender - will it change the genes, too, or are the Sim's kids gonna be as ugly as he was before the "surgery"?
If the latter - is there a way to sync that, too? Or a way to change their looks in-game that will also change the genes?

Genetics won't change when looks are changed after CAS, and it's the same with genetic hair color - just like in real life.

I think there's a way to fix it with SimSurgery in SimPE, but I haven't tried so I don't kow how to. There's probably a tutorial somewhere. You can set new skin, eye color, and probably genetic hair color as well, and I think you can also copy looks from another sim.

There is a tutorial on how to do it somewhere but for the life of me I don't remember where it is.

ADD: Found it.How to change genetics after plastic surgery http://modthesims.info/t/494394

When I open the sim browser, it won't show any sims and I only have the checkboxes "NPC" & "Townie"... anybody got a clue what that is about?

("No meta information" isn't ticked.)

You don't have the neighbourhood open?

No, I loaded the neighbourhood. If I didn't, the sim browser isn't clickable at all.

While we're on this topic,I changed three sims appearance using Sim Surgery in SimPE, so would their facial genetics still be the same or did they change with the surgery

They did change if you used the Sim Surgery in SimPe, yes.