This is indeed a massive problem with GWA (genome-wide association), since the studies only see additive variation. Lot of interesting techniques around to look at non-additive variation. Had acquaintances working on drug-drug interactions and the genetics of skin colour; had to find some cool workarounds.

On the other hand, given that height is closely linked to metabolic conditions, and both the transcription/translation rate and functioning of every cellular component relies on metabolism, it doesn't take long for changes to propagate to simple traits like height.