Do Enemy expansion settings in map generator have any effect?

They affect standard settlements.
In Fixed, "migration" is disabled by default, but there is a "siege" that will provide a certain number of nests next to the player. The "importunity" of sieges depends on the number of nests on the map, expansion settings ignored.

If "siege" and "migration" disabled, only standard settlements will remain.

So if I enable migration there will be new settlements from
A migration state
B siege state near my factory
C vanila expansion which will be effected by the settings
Correct?

yes.
Just in case: if you are going to enable migration, then you should know:
1. After the fixes, migration became too successful (in the standard Rampant, too many settlers settled right where they appeared).
2. When the map is overpopulated, some of the "migrations" become "sieges".
It is not recommended to enable migration: "migration" = survival mode )

I'm a bit affraid that if I don't enable migration I will end up destroying all the hives and then be left with not much to defend against (a bit paranoid after having playtrough with rampant about 6 months ago and almost not getting attacked).

On the other hand since the vanila expansion works I could leave it just to that. (I assume it works only in night if I enable nocturnal mode?)

Edit: I suppose I should mention I'm playing with my borther and he's pretty much dedicated bitter remover.

Oh, there's another big question, who will "eliminate" whom. Catching a player outside the base is one of Rampant's favorite pastimes ).
You don't have to worry about attacks. It is almost impossible to catch all attempts of settlement. And even if you destroy nearby nests, there is a "raid" mode that will attack from afar.

If there are enough resources and there are more than one player, then migration can be enabled.
If a person is alone, there are too many distractions. However, there are a lot of settings - you can always set the difficulty for yourself