"oblique hint, indiscreet suggestion," usually a deprecatory one, 1670s, from Latin innuendo "by meaning, pointing to," literally "giving a nod to," ablative of gerund of innuere "to mean, signify," literally "to nod to," from in- "at" (from PIE root *en "in") + nuere "to nod" (see numinous).
Originally in English a legal phrase (1560s) from Medieval Latin, with the sense of "to wit," introducing an explanatory or parenthetical clause, it also introduced the derogatory meaning alleged in libel cases, which led to broader meaning. As a verb, from 1706.