This is a great web site, but the HMS Victory referred to in this post is not the same ship. The website you included is for the HMS Victory that was Nelson’s flagship at Trafalgar in 1805. I believe it is in dry dock at Portsmouth today. The HMS Victory that will be recovered from the sea bed is its predecessor, which sank in 1744 with all hands lost. Contemporary accounts (one of which is posted above) put its crew at around 1100, which is larger than the crew of the 1805 HMS Victory.
A flagship returning to England following the successful rescue of a blockaded British squadron and merchant convoy would likely be transporting a number of sick and injured from other ships, too.