What are the properties of $item passed in the auto_update_{$type} filter?

It is one element of the response Array that’s a property of the object stored in the update_plugins or update_themes site transient.

That transient looks like this (var_dump()ed):

object(stdClass)#1 (4) {
  ["last_checked"]=>
  int(1519305016)
  ["response"]=>
  array(1) {
    ["akismet/akismet.php"]=>
    object(stdClass)#2 (11) {
      ["id"]=>
      string(21) "w.org/plugins/akismet"
      ["slug"]=>
      string(7) "akismet"
      ["plugin"]=>
      string(19) "akismet/akismet.php"
      ["new_version"]=>
      string(5) "4.0.3"
      ["url"]=>
      string(38) "https://wordpress.org/plugins/akismet/"
      ["package"]=>
      string(56) "https://downloads.wordpress.org/plugin/akismet.4.0.3.zip"
      ["icons"]=>
      array(3) {
        ["1x"]=>
        string(59) "https://ps.w.org/akismet/assets/icon-128x128.png?rev=969272"
        ["2x"]=>
        string(59) "https://ps.w.org/akismet/assets/icon-256x256.png?rev=969272"
        ["default"]=>
        string(59) "https://ps.w.org/akismet/assets/icon-256x256.png?rev=969272"
      }
      ["banners"]=>
      array(2) {
        ["1x"]=>
        string(61) "https://ps.w.org/akismet/assets/banner-772x250.jpg?rev=479904"
        ["default"]=>
        string(61) "https://ps.w.org/akismet/assets/banner-772x250.jpg?rev=479904"
      }
      ["banners_rtl"]=>
      array(0) {
      }
      ["tested"]=>
      string(5) "4.9.4"
      ["compatibility"]=>
      object(stdClass)#3 (0) {
      }
    }
  }
}

So the $item for a plugin update will look like the akismet/akismet.php element in the response Array, meaning you can access the version with $item->new_version.

It is however important to note that there’s zero guarantee that plugins and themes all use the same version numbering system. For example, in a WordPress version X.Y.Z, Y is a major version and Z is a minor version (and X is just for show, apparently), but in WooCommerce X is a major version and Y is a minor version. Every plugin and theme could be different.