Good question. I think there are a lot of reasons.
Most reef tanks are packed to the gills with live rock and corals, so there isn't room for seagrass. They don't grow particularly fast, so they aren't ideal for nutrient export. They aren't widely available. Information on their care isn't widely available either. Though they can coexist in aquariums, corals' and seagrasses' needs are somewhat different. For example, I'm trying to excellerate my seagrass's growth. I'm dosing the water column with nitrate and the substrate with ammonia. I'm fairly certain reef keepers wouldn't be too thrilled about that!
Until we have a better understanding of seagrasses, and there is more information available to us, it seems wise to keep them separately. In nature, you don't see seagrasses growing right on or around coral reefs. You can find small patch reefs in seagrass beds, so I think that would be the best way of combining them in an aquarium.