If Hex causes "disadvantage on ability checks made with the chosen ability", and non-proficient skill checks are effectively just an ability check with no prof bonus added, would those checks be at disadvantage?
Yes, because skill checks are ability checks, proficient or not
You seem to have mistakenly assumed a mechanical difference between a "skill check" and an "ability check" - but understandably so, as in previous editions there was a meaningful difference between the terms. In 5e, all skill checks are ability checks, as per the basic rules (emphasis mine):
Sometimes, the DM might ask for an ability check using a specific skill--for example, “Make a Wisdom (Perception) check.” At other times, a player might ask the DM if proficiency in a particular skill applies to a check. In either case, proficiency in a skill means an individual can add his or her proficiency bonus to ability checks that involve that skill. Without proficiency in the skill, the individual makes a normal ability check.
Proficiency in a skill allows you add your proficiency bonus to relevant ability checks, but doesn't stop them being ability checks. Hex would cause disadvantage on all ability checks involving the targeted ability, whether skill proficiency applies or not.
An important distinction to keep in mind when adjudicating Hex is that attack rolls and saving throws are not ability checks. People usually remember that attack rolls are their own thing, but it's a common misconception that a saving throw is a kind of ability check; however, attack rolls, saving throws, and ability checks are each mechanically distinct kinds of roll, and Hex doesn't hinder a creature's saving throws.
Hex causes the chosen ability's checks to be made with Disadvantage, irrespective of whether the target has proficiency (or expertise!) in a skill with said ability or not. So you don't need to take proficiency into account for this effect.