I'm not sure I've understood you correctly so, forgive me if I've misunderstood you.
Yes. The traits are there, but, they're usually expressed at a very low level. We use controlled mating to increase the expression so that it appears at higher levels and more frequently in the population. We select those that express the trait at higher levels for further propagation and, generation after generation, increase the level that the trait is expressed at.
One of the factors that influences the rate at which we can develop a trait is the time it takes to move from one generation to the next. We call this the selection intensity. With honeybees, we usually test one generation per year when testing for the full range of traits, but, for traits like VSH, it is possible to test 3 generations in a year (but that's pushing it a bit). Other creatures take longer than honeybees to mature though (e.g. cows) so it would take several years to test a single generation.
The way we currently test for VSH is to take colonies that already score highly for hygienic behaviour and subject them (and their progeny) to different tests to improve the level that they express the VSH trait.
I don't mean to make this sound simple or straightforward. It involves a lot of work, but, using techniques like single-drone insemination (sdi), it is possible to develop VSH quicker than it might otherwise take (if indeed it ever did appear) in an uncontrolled mating system.