Prometheus showed how big the ship really was, so she could have just been hiding somewhere inside after filling up the whole inside of the ship. But when two of Ripley's crew went onto the ship itself where would she have been?
Was there ever any suggestion the Engineers regularly carried Queens on the ships?
It seemed they were more often carrying only the eggs. That original crashed ship seen in Alien was probably downed when just one egg hatched and latched onto an Engineer, but then, the 6 people consumed on the Nostromo did not produce a Queen, so a small Engineer ship crew would also probably not produce one.
A Queen emerged on the larger settlement that was founded on the same asteroid as the crashed ship. They had 158 people (157, excluding Newt).
So my conclusion is: Queens were not typically carried on the Engineer ships. If an Alien got loose, it needed a certain size of population to feed on before a Queen could emerge. Neither the Nostromo nor the Engineer ship provided enough food to allow that to happen.
There may not have been a queen at all. It is possible that xenomorphs create a queen when certain limits are reached, in the same way bees do.
See this article https://en.wikipedia.org/wiki/Queen_bee