Propagation... why do I miss some signals?

[cutty]

Which layer of the ionosphere do 16 kHz signals bounce off of?

Also, the idea of a skip zone at such low frequencies is new to me! They are almost unheard of at 2 MHz, and more common as you go up in frequency, depending on the time of day and solar activity.

Any layer or height it wants to.. I suppose.. what does your research show?  Lower freqs bounce. Higher Freqs escape.
You could assume D layer... E maybe at times... I'm an operator, Jim, .. not a physicist.... but, conditionally, the others also have some say about it.  maybe 40-80 miles, whichever is currently 'in charge'... pun intended.

Also do NOT forget:  THE EARTH is the other 'wall' of the wave guide! It makes stuff bounce too.

Unheard of?   You've never listened to a distant am radio station fade in and out?