For example can 5DMKII vs 5DMKIII vs 1DX produce slightly different character of how the bokeh will be formed in the photo when comparing the three full-format-sensors - due to the different mega-pixel-numbers?
Possibly, but if so, it would be a very subtle difference, and likely only evident in some shots.
Is the bokeh from an APS-C DSLR different in quality from the look from a full-frame DSLR´s?
It can be. In some cases, the bokeh is better with an APS-C sensor, assuming you're using an EF (not EF-S) lens. Lens vignetting results in the bokeh of highlights at the edges of the frame having a 'cat's-eye' appearance instead of the more desirable round appearance, and since an APS-C sensor crops away the edges, the vignetting is less and the bokeh at the frame edges is better.
Is the bokeh produced by the super-tele-lenses the most soft-edged, even with the quite "poor" MFD ((Minimum Focus Distance)?
Not really. The supertele lenses are really optimized for sharpness. Lens design is all about tradeoffs. One lens known for particularly good bokeh (often described as 'creamy') is the 50mm f/1.2L. That lens is optimized for bokeh, and the way that's done is to undercorrect for speherical aberration in the lens design. When you do that, you get better bokeh, at the cost of a loss of some sharpness (and some focus shift, too).