This simply does not apply to wheels, the geometry is fixed, rims should not flex vertically ever. A 32 hole box-rimmed wheel is not inherently more comfortable than a 16 hole wheel just because the spokes are under less tension. If your spokes are flexing on your wheel enough to give you a suspension effect, your wheel is going to break. Now the choice of rim may have some effect in the transmission of bumps to your backside, especially with variations of the rim width, but this has more to do with the shape of the tire than anything else.
While I can't explain what is the cause of the differences felt I can assure you however that the difference are quite easily felt.
Since it affects comfort and the relative ease with which a wheel is brought up to speed I assume it must be a minor amount of vertical flex.
Two set of wheels that are much alike in build but differ mainly by their rims are Campagnolo's Neutron and Hyperon.
The main difference being the rim material.
While I won't complain by saying the Hyperons are not comfy, they are, the Neutron are simply on another planet when it comes to being comfortable.
I'm sure there must be other examples out there.