Whatever works for you ... don't trust the generalizations of some anonymous people who don't know you. If you have problems with your knees, such as old sports injuries, or arthritic knees, etc. ... it would be imprudent to kneel on "bare floors" or even the un-padded wooden kneelers. In fact, even if your knees are in good shape, kneeling on hard surfaces can cause damage over time. Other things can be done for penance that don't involve potentially damaging your joints. Our Lady instructed the children to stop certain penances they had undertaken since it could have caused them physicla harm.
So the answer to your question is entirely subjective, analogous to how some people sleep better on softer mattresses, but then other people hurt their backs on soft mattresses. It all depends on your physiology, how you tend to position your body when you sleep (sides, back), and whether you have other issues (back or knee pain etc). Again, you could sanctimoniously declare "just accept the penance", but then if you're not getting enough sleep, that can cause emotional, psychological, and even spiritual issues (+Lefebvre insisted on seminarians and priests getting sufficient sleep ... and I'm sure he knew cases where some had "cracked"), or if you don't sleep on the right surface, you might wake up and then barely be able to walk or function or do your job (especially if you do manual labor).
This is why Prudence is considered the Queen of the Virtues, where you have to weight and take into consideratin many different factors. No, doing as much penance as possible in all areas is not some absolute good, and savors of that leaven of the Pharisees. Instead, sometimes various penances can do more harm than good, or are done for the wrong motives, e.g. pride, something that offends God more and keeling on a cushion or even just sitting down. That's yet another reason why it's important to obtain good spiritual direction if possible. Otherwise, use sound judgment while not turning things that are relative, ends to various means, as if they were ends in and of themselves.
By orders of magnitude the greatest moritifcation should be of one's pride, and doing things only under obedience to a director helps offset that. People aren't given to pride, for instance, when they abstain from meat on Friday because they're doing it out of obedience to the Church's law. In this, for instance, if you were to opt for some thick cushions, you could humble yourself by declaring yourself inferior to those who can keen without them, and that would please God much more than someone thinking highly of himself for kneeling on a bare floor.