Just a quick confirmation - today's update 4.9.88-1+deb9u1 fixed the boot timeout for me.
-- Miroslav Kure
- Bug#897632: Boot timeout after latest security ... Miroslav Kure
- Bug#897632: (Boot timeout after latest sec... Miroslav Kure
- Bug#897632: marked as done (Boot timeout a... Debian Bug Tracking System
