Ya it’s definitely frustrating that those options disappeared.
To disable Notifications I went into the database in the end and edited the serialized array for the jetpack_active_modules option in wp_options table.
As it’s a serialized array you have to make sure you’re updating the array count at the beginning when removing the items. Notifications are called notes in that array.
Example
BEFORE
a:19:{i:0;s:18:"after-the-deadline";i:1;s:20:"custom-content-types";i:2;s:10:"custom-css";i:3;s:21:"enhanced-distribution";i:5;s:8:"json-api";i:6;s:5:"latex";i:7;s:6:"manage";i:8;s:5:"notes";i:9;s:10:"omnisearch";i:10;s:13:"post-by-email";i:11;s:9:"publicize";i:13;s:10:"shortcodes";i:14;s:10:"shortlinks";i:15;s:5:"stats";i:18;s:17:"widget-visibility";i:19;s:7:"widgets";i:20;s:8:"carousel";i:21;s:6:"photon";i:24;s:13:"tiled-gallery";}
AFTER
a:18:{i:0;s:18:"after-the-deadline";i:1;s:20:"custom-content-types";i:2;s:10:"custom-css";i:3;s:21:"enhanced-distribution";i:5;s:8:"json-api";i:6;s:5:"latex";i:7;s:6:"manage";i:9;s:10:"omnisearch";i:10;s:13:"post-by-email";i:11;s:9:"publicize";i:13;s:10:"shortcodes";i:14;s:10:"shortlinks";i:15;s:5:"stats";i:18;s:17:"widget-visibility";i:19;s:7:"widgets";i:20;s:8:"carousel";i:21;s:6:"photon";i:24;s:13:"tiled-gallery";}
Hope that helps until Jetpack and re-introduce those options.
Leaving this unresolved as this is a workaround and not a proper resolution.
Cheers