I'm modding in various melee skills, though they mostly aren't strictly monk-like. Stuff like shove, grapple, a short distance leap. But also a "quivering palm" skill. Unfortunately there isn't really a way to check if a character is unarmed in the skill data entries themselves. As Wouter suggested, you could sort of fake it with a check for a staff weapon or something, and add "invisible" staff weapons that deal physical damage. But you could still use regular staves in this case. I'm probably just going to add physical damage staves and require staff weapons for a monk class.
There may be a way to script a check if a weapon is equipped, but I can't think of a super simple way to do that. If this is possible, skills could have additional effects when used when unarmed, and would still work if used with weapons, which I think is a good balance.
I don't have enough skills for a full monk class, so will probably just throw these skills into warfare. What kind of skills do people expect for a monk class that are actually mechanically unique and not basically just warfare skill, except with your fists? Ultimately, I think monks are much more about flavor and roleplay than adding a true gameplay niche. I think of monk as more agile than warriors, but tankier than rogues, and dealing less damage than each, but having certain utility and disable options that rogues and tanks don't have.