In alien isolation you can see all the eggs but where is the queen?
There isnt always a queen, like in the first movie and some of the comics, the Xenomorph drone is capable of creating hive resining, which can change a living organisms compound to a overmorph egg which contains the facehugger. :)
Except Creative Assembly (the devs) did say that there was a Queen, they just didn't want the player to encounter or see her as the player would then expect to fight her.
That is an excellent question
The devs said she's in the ship, but the player never finds her.
I got an idea maybe she was on the ship but somthing killed her and her body fell out into space
What do you think?