Do I have to consider the water in the hydrate of a salt in a mass percent calculation?
As stated in one of the comments to your question, the waters of hydration constitute part of the crystal structure itself, just as much so as the rest of the molecule. You can somewhat think of the waters as being functional groups of the compound. For example, the dehydrated form of a compound can have very different chemical and physical properties than the hydrated form.  The presence of waters of hydration in no way means that the compound is aqueous or dissolved in water.  

Thus, when calculating the mass percentage of hydrogen of the hydrated compound, you do include the hydrogens from both the waters of hydration and the rest of the molecule.  

The common name of  $\ce{NH4MgPO4⋅6H2O}$ is magnesium ammonium phosphate or struvite. According to this Wikipedia article:  


  Struvite (magnesium ammonium phosphate) is a phosphate mineral with
  formula: $\ce{NH4MgPO4·6H2O}$. Struvite crystallizes in the
  orthorhombic system as white to yellowish or brownish-white pyramidal
  crystals or in platey mica-like forms. It is a soft mineral with Mohs
  hardness of $1.5$ to $2$ and has a low specific gravity of $1.7$. It is
  sparingly soluble in neutral and alkaline conditions, but readily
  soluble in acid. Struvite urinary stones and crystals form readily in
  the urine of animals and humans that are infected with
  ammonia-producing organisms.  


Here is a photograph of struvite crystals from the same article: