When the Horse was left at the gates of Troy could they not see all the ships on the horizon and think something was up? Where was the army that bumrushed Troy?

The horse wasn’t necessarily historical. It could have been an allegory or some historians may have been confused about war terminology of siege engines.

As for the sailors hiding? Look at a map of where Troy is. It’s just inside the Dardanelles which is a strait linking the Aegean and Black Seas. The navy could have waited in the Aegean and sailed in at a predetermined time.