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One great online resource for this type of question is if you search for 'ineffable' there, it tells you that that word isn't as transparent as one might think. It comes from Latin 'ineffabilis', where the base isn't 'eff', but 'effari', which just means 'to utter'. 'Ineffably' thus literally means 'inexpressible' or 'too great for words', with which 'not to be understood deeply' is connected.

Generally in etymology, you do not find the strategy of word formation you imagined - it would be unexpected/weird for the base of a word to be such a euphemism, especially if the word hasn't cropped up only recently.