Hi The Trope!
About FX there are two main approaches:
One is to have them directly inside Spine so that they match the skeleton and animation perfectly, another one is to use a combination of emitter bone and events to generate them at runtime. so it mainly depends on the size and specificity of your skeleton.
Since as you said there's no out of the box solution, it's hard to answer this question without seeing what style you're gonna use for the drawings themselves. Also, a problem I encountered is that some weapons require a different way to be hold.
A solution could be to make all your animations in a version without weapons at first, and then create variations of those animations by using for example a transform constraint that links the hand to the weapon, so you just need to animate the weapon movement and the hands will follow, with the possibility to lower the constraint if needed. Still, I guess this is still painful to animate if you have a lot of animations,
maybe you could group weapons in 2-3 macrogroups based on how the have to be hold and make the custom animations just for that. If you also need to have fancy effects on the weapons you can have a couple bones to be used only when needed.
Also, about the different skeletons, you'll probably have to redo some parts to adapt them, but apparently in the beta you can now copy bones between skeletons 😃
In conclusion, with more information we could give better advice, but yeah you wrote down the possibilities yourself.