This behaviour was a bug.
This “enumerate every 3 seconds” thing is implemented to support hotplugging (=> detecting new devices or if existent ones have been unplugged) - but it should only be used in case the operating system can’t tell you about those events.
Not sure which operating systems support/don’t support sending you plug/unplug-events, but Windows certainly does support it, so it shouldn’t happen (on Windows it should only be used if telling Windows to send those events failed).
The bug in 2.0.9 is basically that if you don’t activate joysticks via SDL_Init(), the internal flag for “operating system will send events” is not set, and because of that the frequent enumerations are done (the fix was to not do those enumerations at all if joysticks aren’t enabled).
So one possible workaround (if you want to use unpatched 2.0.9) is to pass SDL_INIT_JOYSTICK to SDL_Init(), even if you don’t otherwise use/support joysticks. (I think doing this shouldn’t “hurt” or cause additional events, because you should only get input events from joysticks if you have enabled a particular joystick with SDL_JoystickOpen() or SDL_GameControllerOpen().)