The data used to create these listings combines information from the Quinquennial and the Mercantile Navy lists. By doing this, you find only the vessels actually registered in Yarmouth, irrespective of their whereabouts at the time of the survey.
It is relatively easy to extract lists of vessels from the various census documents, as has been done at SHIPS IN UK PORTS 1881 on Angelfire (beware of popups!). However that way you will find only those ships that were actually in port on the day of the census, irrespective of their port of registration.
There is an explanation of much of the holdings on mariners at the PRO (Public Records Office, UK) and other places at the MARINERS website.