Hyperflexibility, or hypermobility, can be physiological, as it can be caused by connective tissue disorders, such as Ehlers-Danlos syndrome. Some people without any known abnormalities of connective tissue are nevertheless quite hypermobile, so probably have differences in their connective tissue to the rest of the population, but suffer no problems from this, and may even find it an advantage in some sports.
Hypotonia, or low muscle tone, can also cause hypermobility, as the muscles do not effectively support the joints, allowing the ligaments to become over stretched. Hypotonia has multiple possible causes, some physiological, but some are neurological as opposed to being caused by abnormalities in the muscle fibres themselves. Hypotonia and hypermobility are not uncommon findings in dyspraxic children. If your ds doesn't bruise easily, scar badly, have unusually stretchy or translucent skin, dislocate joints easily or have other such physical symptoms besides the hypermobility, it's unlikely they'll look into whether the cause is physiological or neurological, as it wouldn't make any difference to the treatment.
Are other members of your family hypermobile? My son is hypotonic and hypermobile (as yet no diagnosed cause and no other glaringly obvious symptoms). I and other members of my family are hypermobile, but it's never caused any of us any problems and we're not hypotonic in addition. I feel that my son has been unfortunate enough to inherit my hypermobility and in addition is a bit hypotonic, which exacerbates the hypermobility to the point where it is a bit of a problem for him and every joint in his body is hypermobile, although we haven't yet seen the neurologist and geneticist to rule out a connective tissue disorder or myopathy, either of which are unlikely as they are very rare. I have a feeling that his hypotonia is neurological/CNS in origin, but I'll probably never know.