I've tried to find tutorials on this, but I didn't find anything. I have long lists of 10,000+ names and surnames and I want to use those in my game instead of the EA ones. I have the Czech version of the game and those names are ugly.

From what I've gathered online you need to use .stbl and .csv files, but I have no idea where to get the .stbl or how to get the hex values into the csv. Do programs like S3PE automatically generate those values once I input the name? And how does the game differentiate between a female or male name and surnames?

I also tried to download other people's name replacement mods and copying my names into them, problem is that there aren't enough of those "key" components (the ones that have the byte number value) for all my names to add.
The Nraas SP Name Tuning doesn't work for me for some reason and I've tried enabling it via the immigration option, but it's still not the thing I want.

The description of the tool that uses those formats, STBLizer , already has template name replacement files and instructions for them attached to the post

Is it possible to have too many names? Because I put my .csv file through a validator and it said it should have between 0 and 10,000 characters.

Yes- you'll have to reduce your list to fill the exact number of keys that are available.
1010 female names, 1037 male names, and 3127 surnames that are doubled for male/female (a total of 6254).

Adding more keys to EA's script tables would require a more advanced mod- but you could add the full 10k to StoryProgression's name tuning so that they are used some of the time.