When sanding saddles I usually hold the saddle up against the side of a metal spirit level to keep it at 90 degrees to the sandpaper. BTW, there's no significance to the fact that I use a spirit level other than it's a convenient size and shape...
Another consideration is that the way many people hold the saddle when sanding puts more pressure in the centre area of the saddle. If you put the saddle on a flat surface and sight underneath it you may sometimes find that that extra pressure to the middle has resulted in you taking more material off the middle of the saddle base - you'll see a slight concavity there.
It's easily remediable by ensuring that even pressure is applied along the length of the saddle. If you leave it, especially if you have an undersaddle pickup, then you may find that the volume of the middle string courses can suffer as the bridge presses down less firmly beneath them.
Funny thing is that this doesn't seem to happen on mandolins, where there is often a deliberate gap under the middle section of a bridge, but on ukes I've experienced it several times.
It's good to see people trying this stuff out.
EDIT: Thinking about it, it's not that surprising that the bridges on the two instruments behave differently. Gibson style mandolin bridges are subject to simple downward force, whereas uke bridges endure a much more complex set of twisting and sheering forces...
I'll get me anorak...