The 100 km/h updrafts from the ground would be very strong effect—nearly hurricane strength already! I'm not a weather expert, but depending on how large of an area the updrafts would exist in (and how densely packed your islands are), this could indeed create a lot of other dangerous eddy currents that could result in some very strange weather indeed.
These updrafts would also cause a big, direct problem for anything that needs to fly via conventional lift mechanics (including non-magical airplanes and birds). The thought of some poor flock of geese getting violently splattered on the underside of one of these islands is not a pretty thought. I suppose you could have the flighted animals evolve a little better awareness of subtle pressure changes or island shadows and navigate around them.
Honestly the best way to deal with the overall weather/wind issue would probably be to just reduce the wind strength significantly. If that's not possible, then the next best thing I could tell you is to perhaps have the effect start at a higher altitude (at least a few hundred meters off the surface), and at a gradual gradient, or maybe with some kind of magical barrier to prevent the wind from creating "spin off" currents. (My bad weather puns, you can have for free.)
The top end altitude for rain clouds is about 2 km. You're going to struggle to get any water at all up there at your altitude of "a few km".
If you can lower your islands, great. Otherwise, they'll either need to be big enough to support their own water cycle (how big, I'm not exactly sure, but big: they'd need to retain at least a large lake/small sea worth of water and have a very large and mountainous land area to support wind patterns and temperature/pressure differentials), or you'll need to come up with some magical high-altitude rain clouds.
If you can get rain, and have enough soil depth and large-scale dips in the surface (lakes) such that it doesn't all run off immediately, you'll at least be able to keep water around long enough for it to be useful for plant and animal life.
Erosion is going to play a big role; water is going to tend to carve out rivers with time, and there's a good chance that one or two large rivers are going to dump all of the water off of the island, and it's all going to land in one spot. Fortunately all that water is quickly going to hit terminal velocity (about 200 km/h) on the way down so it won't instantly start carving huge canyons, but it's still going to hit very hard if a lot of water is concentrated in a relatively small area.
Alternative Water Sources
Irrigation is an option, although you will need either a very powerful multi-staged mechanical or magical pumping system to move water up by several km. Could create some interesting trade opportunities if, say, the lowlands have a monopoly on water, but the island people have a monopoly on other resources like sunlight crops, wind, or whatnot.
Big islands create big shaded areas. Plants on the surface might suffer a bit if there are a lot of these islands, especially if they don't move around independent of the surface. Something to keep in mind, not an insurmountable issue.