One large autoloaded option is on every single request

The failure mode is not a slow query. It is one option holding a megabyte of serialised data, fetched and unserialised on every request, quietly adding both to the memory floor and to the time before anything renders.

wp db query "SELECT option_name, ROUND(LENGTH(option_value)/1024) AS kb
  FROM wp_options WHERE autoload='yes'
  ORDER BY LENGTH(option_value) DESC LIMIT 10;"

Common culprits are plugins caching remote responses in an option, licence checks storing a full API payload, and any log written to wp_options. Flipping one to autoload = no is a single UPDATE and safe if the plugin reads it through get_option(), which it almost certainly does — the flag only affects whether it is preloaded, not whether it can be read.