Is (S)-3-hydroxypalmitoyl-CoA a hydroxy fatty acyl-CoA?
This just looks like an arbitrary distinction they made in the ontology between 'short chain' acyl-CoAs and 'long chain'. As you can see, the 3-hydroxypalmitoyl chain is somewhat longer (16C) than the others. It stands to reason that the creators of the ontology have decided to subdivide hydroxy fatty acyl-CoAs into those with shorter hydroxyl fatty chains:


hydroxyoctanoyl:   8C
hydroxydecanoyl:  10C
hydroxylauroyl:   12C


and long:


hydroxypalmitoyl: 16C


As to where the dividing line is, the hydroxytetradecanoyl-CoA (14C) homologue is not 'long chain', whilst there is no entry for hydroxypentadecanoyl-CoA. The octadecanoyl homologue belongs to its own class (of 3-hydroxyoctadecanoyl-CoAs, of which there are only two conceivable enantiomeric members), and there does not appear to be icosanoyl homologue in the database. There may be other members of the 'long chain' family if you search around, who knows?

In short, it appears to be arbitrary.