I agree that there is nothing that tells us if the combat skills scale with ATK or MATK but with common sense you would probably come to the conculsion that they do since they are all based on physical attacks and there is a specific section called Magic so Magic Attack (MATK) would seem to only affect magic spells/skills. I don't think it's a big deal but it wouldn't hurt the game if there was something in maybe the skill description that tells us what stats that affect them.
As for the skills and stats: I think the incease is by a small percentage so you can't really see much of a difference when leveling up skills. Same goes for stats as they won't affect your damage much (going from level 1 to level 2 makes no difference in how many attacks you need with a 1h sword to kill a Slime or a Rabby). To see the actual numbers seem useless to me (even if it would make decision making easier) as it wouldn't really add anything to the game, it would just provide the tools you need to involve maths in your skill decisions. To me personally it wouldn't really matter as I've already found my prefered skills but for new players the stats might "force" them to choose a skills they think seem less appealing because the stats are way better. Going for style rather than stats seems like the general approach in this game so I guess keeping it as it is would follow the current structure (Maybe???).
Right now you gain a lot of skill points so eventually you reach this point where you go "Hmm, I've used 5 bronze points in this skill I like and now I have 15 more of them that I haven't used... Let's try some new skills!" and off you go. Even if you make the decision to spend a lot of points on one skill you will always end up with spare points (unless you have a very diverse build that uses more than 4-5 skills.) Also, right now (and this might just be my opinion on the matter) you don't really spend skill points to get the +damage for your skills, you spend points to unlock the next charge for it. The change in damage us huge (on some skills at least) between the charged vs non-charged skills. Cloud Strike is a good example of a skill that gets better when you reach a new charge for it while skills like Earth Spike don't really gain much (DPS) from the extra points. To get back on the topic again, the +damage numbers would be pretty useless as you don't want level 2 or level 8 skills, you want bronze, gold, normal, silver or final charged skills.
If you disagree with me then feel free to let me know. I'm just stating my opinion.