I think the plants will get (most of) the fertiliser when you water, but I think the mulch will get some too. Since the fertilizer will be a source of nitrogen, applying it on top of mulch will probably speed the decomposition of the mulch. You might see this as a good thing or as a bad thing.

IMO, move the mulch, apply the amendment, then put the mulch back. Feed the soil, not the mulch...

Blutranes

Put them on top of the mulch and the Soil food Web that is starting to work in your planitng beds will move that into the soil for you, although it may well take more time than you would. There is no need to move your mulches.

+1 what Kimmsr said.

Another point to look at, that I recently read, is that when mulches begin to self compost on top of your soil, they begin to consume nitrogen themselves pulling out of the soil...essentially stealing it from the plants.

Fertilizing on top of the mulch would likely curb this phenomenon...

Either way works. Your mulch will probably disintegrate faster if you put it on top- I'll go ahead and guess. I personally like composting the mulch in place because of what it does for the soil.

Keep up the mulching- it will not only reduce weeds, but will conserve water and keep soil moiture at a more constant level (most plants appreciate this- especially fruiting plants).

Depends on the type of mulch as to how much nitrogen depletion may occur. Wood based mulches tend to require greater activity and longer time for the soil organisms to breakdown and so they use up some of the available nitrogen in the process. But unless the mulches are incorporated into the soil, nitrogen depletion will occur only at the soil surface where it is most easily volatized and not heavily present anyway and have little to no effect on the deeper feeder roots of most plants.

Mulches, material placed on the soil surface and not mixed into the soil, will not "rob" Nitrogen from the soil. Thre is ample research to support that and none at all to support the contrary. When someone has "seen" this happen we find they actually have made the mulch into a soil amendment by mixing it into the soil.
A mulch is never mixed into the soil, but a material intended to be a mulch can become a soil amendment simply by stirring it into the soil.