I was checking out (through SimPE) the Sims from a neighborhood, and I noticed that a ghost had Nightlife flags (turn-ons and turn-offs), but all the others did not. I also noticed that this same ghost had no genetics of personality, and all the others had. Are these errors by the creator of this neighborhood (in this case, EAxis)? If I add this information to Sim through SimPE, is there any chance that I will corrupt the neighborhood or the Sim?

Is this a base game hood? If so the Sim in question is probably one with a linked character file (e.g. Michael Bachelor, or the ghosts in Olive Specter's graveyard). They are full Sims, though many of them are missing data like personality and genetics. The others are unlinked and missing data, which you would have to reconstruct before altering them further. You can tell which Sims are unlinked in SimPE as their portrait has a blue background.

Additionally, if the ghosts have not been spawned in the world, then they may not have had EP attributes initialised for them yet. It should be enabled as soon as they appear on a lot for the first time.

There is always a small risk of things going wrong, so you should always keep a backup, but the process of editing these attributes itself shouldn't cause problems.

(And if it's from my version of Strangetown, do let me know as I've probably missed them out when going through the ghosts and fixing their genetics )

By now, I can't tell if all ghosts have this genetics problem, but I know Knut Futa is one of them.

Knut Futa is truly broken. Maxis did a real number on him by wiping virtually all of his data except for his appearance.

I restored him in my version and the changes seem to have taken in my game, except for his personality, which is always randomised for some unknown reason.

Oh, yeah... It's easier create a completely new Sim exactly like Knut and replace him with the copy than restore the original perfectly.
I also noticed that some ghosts have only the "It's a Ghost" flag, but not the others. Maybe it's because they have no tombstone?

That's correct, although most of the pre-made ghosts are missing the flags when they should have them.

Oh...

Okay, new "Maxis being Maxis" error: the Curious twins (alien ones) don't recognize the Curious brothers (humans) as their stepbrothers (part of the family), so they can fall in love, go Woo-Hoo, get married and have a child. Yes, that is creepy. I'm not sure, but I think this happens with other families (I will investigate it).

OFF-TOPIC: I think that a "Veronaville fixed version" would be cool too, because Veronaville and Strangetown were the neighborhoods made before Maxis change the code of the game. They don't correct the neighborhoods. I didn't played that one very much, but I know that there is a lot of "time concordance errors" (see it here) and some glitches like missing data, corrupted faces, etc.

I do plan on doing Veronaville next, and then Pleasantview. I've made lots of notes on things that are wrong with them. Just taking a break from it first since Strangetown was quite time consuming to go through and fix.

Cool! I would love to test them too.