Hi Cate! This is a normal part of updating and is quite short. I honestly wouldn’t worry too much about SEO, but you could let your members know that you update frequently so they know to just check back later if the site appears to go down for a few minutes while you are updating.
Also, if you update from the UI the site will remain mostly available during the update.
There is a trick to show an “under maintenance” page while updating but I don’t recommend it.