The titular words are etymologically related only by mistake. Impregnable, formerly imprenable, comes to English from the Old French imprenable and means unable to be captured or broken into. Impregnatable, however, comes from the Late Latin impraegnatus and means to make (a female) pregnant or to be able to be permeated.
The added g in impregnable, and the subsequent confusion between the two words, can be blamed on unknown Renaissance-era philologists, who likely mistook the word as a relative of pregnant.