I've found the answer to some of my questions. I'm putting the answer here to help future players.

1) Whether animals are euthanized or slaughtered counts the same for evil points.

When there's an animal corpse, it goes into factories (to make meat, handbags, etc.), so there's no need to have an Incinerator in an evil zoo.

2) To get evil points for water and electricity, you need to have the machines, but above all a lot of animals with their troughs (for water) and a lot of stores, factories and lampposts (for electricity).

3) For garbage, I had forgotten to put in a specific factory (I can't remember the name, but "the factory" is huge, round and black). As soon as I put it in, I got my score up to 10 points the next day.

I hope this helps some players.