Kickboxing, first of all, is a different game all together. Big gloves and kicks and NO takedown threat changes the style completely. Less head movement etc. Also, keeping your hands up is the first thing you learn because it is the easiest defense to learn. That doesn't mean it is applicable in all scenarios and in all fighting sports.
Just look at early boxing with smaller/no gloves, and where more clinch (or even throws) was allowed. The style looked a lot more similar to mma, than boxing.
Keeping your hands down increases your ability to find shots and see shots coming (both striking AND wrestling btw). If you do one offs, yes then it's a good idea to keep your other hand up, but you can't do that with combos. Also, keeping your hands down make it harder for your opponent to see when a punch is coming since the movement is different and there is less of a wind-up (if done properly). There are different defenses also, like the shoulder up/chin down, or raising your arms straight out to defend against hooks (Gus likes this).
Point is that there is a risk/reward scenario, and you can't just "put your hands up" and expect that all your problems will be solved.
It doesn't mean you should NEVER keep your hands up, just that the mantra is overused and misunderstood by every Tom, Dick and Harry.
Speaking of Machida, even though he isn't perfect, he sure doesn't get hit a lot while having his hands low. Neither does Jones - he doesn't really rely on keeping hands up but on distance and clinch. A good example of a BAD applications of hands up is Struve, who has the added disadvantage of having long arms and thus not being able to cover up properly.