Your question is pretty valid as two children have similar problems. Yes, there are many genetic conditions which run in families and can cause hypotonia. The various causes could be: congenital hypothyroidism, Charcot-Marie-Tooth disease (a demyelinating inherited condition), Down's syndrome, Prader-Willi syndrome (a rare genetic condition which affects growth and learning along with many other symptoms), Tay-Sachs disease (this is a fatal progressive disease affecting the nervous system and hence it is unlikely that your son's suffer from it), spinal muscular atrophy, myasthenia gravis(your sons' are unlikely to have this problem so early in life unless you suffer from it), and muscular dystrophy.
There are two other conditions which affect the connective tissue and hence cause hypotonia and hypermobility and these are: Marfan syndrome and Ehlers-Danlos syndrome.
So, it is important to get a genetic counseling and follow this aspect of cause behind your sons’ problems. Please discuss with your doctor. Good Luck and take care!