hook_boot() is only used by test modules in core now. Previous uses of hook_boot(), ban module, statistics module etc. are doing things properly - either with an event listener if they only care about interrupting the request, or with an ajax callback if they care about running on cached pages.
if we remove hook_boot() and refactor a couple more bootstrap hooks, we can remove that concept altogether and simplify both bootstrap itself and the module system a fair bit.
There is one remaining use for hook_boot(), which is where you just want to run some arbitrary code as early as possible, for example devel's xhprof support or similar. For that, I think we can tell people to copy/paste some code into settings.php since those are pretty rare cases.