When a user doesn't have the moodle/my:manageblocks capability, or when $CFG->forcedefaultmymoodle is set, they cannot see any items on their /my/ page.
This was not an issue pre-2.9.

The problem is that when you edit indexsys.php, it creates DB entries with 'showinsubcontexts' set to 0 and with a 'subpagepattern' of 2. This means the SQL to find page blocks for the current user in `function load_blocks` (blocklib.php) never matches them.

The page is always set to your user's context if logged in. The SQL in load_blocks looks for things with your user's context or that shows up in subcontexts, and can't find anything.
It also checks for a subpagepattern of NULL but because they're all '2', it filters everything out.