3-4% of one magnet missing - I don't think you'll notice any difference.
You should try to get the spacing as precise as possible, or uneven performance and possibly excess noise will be the result. I don't know what the spacing should be, but you can probably guess by looking at it; use matches as spacers, or cardboard if there's little space.
It's very important not to remove any magnets and mix them before you glue them back; the have to be in the right order! (North/South poles in the right order.) Glue one by one.
And BE CAREFUL! I'm guessing it's Neo magnets, and they are rather powerful buggers; they'll nip your skin easily if they come together, and can splinter if they're hit hard... (By getting attracted to each others for example...)
But let others here tell you if they're really glued or not; I think they should be, but i've never opened any of those motors... Made some windgenerators with neomagnets though, and one doesn't want any loose magnets there...