The padded sets make it very apparent that monster bonuses are underpowered:
1) Monster bonuses do not stack past the general damage cap
2) Two undead medium bonuses will surpass the cap with a peacemaker
3) Two mixed monster bonuses from padded armor will give you a medium bonus against two families, while a pure general purpose set gives you the same bonus against six
The third point makes it fairly obvious that mixed monster bonuses aren't worth it, and the previous two should make it clear that pure monster bonuses aren't really worth it either, even in levels with just one monster type. At least with a peacemaker, a regular shade helm with ghost armor will be doing just as much damage to undead as someone with a full ghost set would.
Medium monster bonuses need to be raised to high, and they should stack past the cap, at least to +9 (current max is 6). This would make them worthwhile compared to general bonuses, and allow you to wear full deadshot with a peacemaker which I think obviously you should be allowed to do. I think this goes for more than just the gunner sets though; something like a deadly virlisk mask is similarly giving up something like a medium sword damage bonus compared to sklover, etc, so the comparison still applies.
Admittedly the virlisk set's monster bonus isn't weapon-specific like with the padded armors (nor is deadshot's), but if you're running mixed weaponry you're probably only going to use one of your weapons against each monster type anyways, so close enough; it, along with the medium bonuses on the dragon, valkyrie, silvermail etc may as well be raised to high. Fallen's penalty could be too, fiends aren't present in void levels anyways. The divine set should also probably get raised to high and get a bonus on its armor. As for the shadow lair armors with low bonuses, beats me. They have other problems.
Do you intend for the monster bonuses to stack like they currently do with universal bonuses? E.g. if I wear black kat set (+6 for everything against everything) and equip a pet perk vs undead (+3 for everything vs undead), will I total +9 for everything vs undead? If so, I think your suggestion would lead to everyone still running black kat, except that damage bonus vs monster UVs on weapons become much more powerful (and a must have if you want to have a top tier loadout). Perhaps that is not a bad thing, since it evens out the value of weapon UVs. I don't think it will balance armors though because getting to +6 and +2 MSI with black kat is still better than everything else.
I don't have time to think more about it atm, but I like that you at least still included a cap for monster bonuses. Damage bonus is the most important modifier in spiral knights and there's a reason it is capped. I agree monster bonuses deserve a bit of a buff, and +9 is probably not too high to be completely game breaking. I personally already use monster bonuses very often, and it is worth it because you can stack your defense much higher when you use a specialized defense. However it is also much easier to just use black kat, and the fact that you cant replace the MSI if you don't is at least equally disappointing.